All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=400, mem_mb_total=200 Select jobs to execute... [Tue Nov 19 04:46:24 2024] rule rule_1_combined_fastq: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group2_LPS1/Group2_LPS1_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group2_LPS1/Group2_LPS1_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_LPS1/Group2_LPS1.R1.combined.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_LPS1/Group2_LPS1.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/1_combined_fastq.Group2_LPS1.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=400, mem_mb_total=200 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/ExtractBCSR.py --fastqIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group2_LPS1/Group2_LPS1_R1.fastq.gz --fastqUMI /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group2_LPS1/Group2_LPS1_R2.fastq.gz --fastqOut /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_LPS1/Group2_LPS1.R1.combined.fastq.gz --bcHistFileName /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_LPS1/Group2_LPS1.umi_frequencies.csv > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_LPS1/Group2_LPS1.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/1_combined_fastq.Group2_LPS1.txt [Tue Nov 19 04:56:16 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Tue Nov 19 05:03:10 2024] rule rule_3_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_LPS2/Group2_LPS2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group2_LPS2/Group2_LPS2_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_fastqc.Group2_LPS2.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS2 threads: 5 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group2_LPS2 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group2_LPS2 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_LPS2/Group2_LPS2_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_fastqc.Group2_LPS2.txt 2>&1 [Tue Nov 19 05:03:45 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Tue Nov 19 04:59:22 2024] rule rule_2_cutadapt: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_LPS2/Group2_LPS2.R1.combined.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_LPS2/Group2_LPS2_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/2_cutadapt.Group2_LPS2.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS2 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -j 4 --times 2 -u 1 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_LPS2/Group2_LPS2_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_LPS2/Group2_LPS2.R1.combined.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_LPS2.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/2_cutadapt.Group2_LPS2.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_LPS2/Group2_LPS2_R1.fastq.gz.deleted [Tue Nov 19 04:59:59 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1011, disk_mb=1011, mem_mb_per_thread=400, mem_mb_total=200 Select jobs to execute... [Tue Nov 19 04:46:25 2024] rule rule_1_combined_fastq: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group2_LPS2/Group2_LPS2_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group2_LPS2/Group2_LPS2_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_LPS2/Group2_LPS2.R1.combined.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_LPS2/Group2_LPS2.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/1_combined_fastq.Group2_LPS2.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS2 resources: mem_mb=1011, disk_mb=1011, tmpdir=/tmp, mem_mb_per_thread=400, mem_mb_total=200 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/ExtractBCSR.py --fastqIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group2_LPS2/Group2_LPS2_R1.fastq.gz --fastqUMI /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group2_LPS2/Group2_LPS2_R2.fastq.gz --fastqOut /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_LPS2/Group2_LPS2.R1.combined.fastq.gz --bcHistFileName /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_LPS2/Group2_LPS2.umi_frequencies.csv > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_LPS2/Group2_LPS2.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/1_combined_fastq.Group2_LPS2.txt [Tue Nov 19 04:59:07 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1033, disk_mb=1033, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Tue Nov 19 05:25:32 2024] rule rule_3_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_C1/Group1_C1_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group1_C1/Group1_C1_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_fastqc.Group1_C1.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C1 threads: 5 resources: mem_mb=1033, disk_mb=1033, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group1_C1 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group1_C1 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_C1/Group1_C1_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_fastqc.Group1_C1.txt 2>&1 [Tue Nov 19 05:26:16 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1002, disk_mb=1002, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Tue Nov 19 05:03:21 2024] rule rule_2_cutadapt: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_C1/Group1_C1.R1.combined.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_C1/Group1_C1_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/2_cutadapt.Group1_C1.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C1 threads: 4 resources: mem_mb=1002, disk_mb=1002, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -j 4 --times 2 -u 1 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_C1/Group1_C1_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_C1/Group1_C1.R1.combined.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_C1.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/2_cutadapt.Group1_C1.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_C1/Group1_C1_R1.fastq.gz.deleted [Tue Nov 19 05:04:07 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1289, disk_mb=1289, mem_mb_per_thread=400, mem_mb_total=200 Select jobs to execute... [Tue Nov 19 04:46:24 2024] rule rule_1_combined_fastq: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group1_C1/Group1_C1_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group1_C1/Group1_C1_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_C1/Group1_C1.R1.combined.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_C1/Group1_C1.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/1_combined_fastq.Group1_C1.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C1 resources: mem_mb=1289, disk_mb=1289, tmpdir=/tmp, mem_mb_per_thread=400, mem_mb_total=200 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/ExtractBCSR.py --fastqIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group1_C1/Group1_C1_R1.fastq.gz --fastqUMI /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group1_C1/Group1_C1_R2.fastq.gz --fastqOut /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_C1/Group1_C1.R1.combined.fastq.gz --bcHistFileName /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_C1/Group1_C1.umi_frequencies.csv > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_C1/Group1_C1.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/1_combined_fastq.Group1_C1.txt [Tue Nov 19 05:00:15 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Tue Nov 19 05:00:41 2024] rule rule_3_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_C2/Group1_C2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group1_C2/Group1_C2_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_fastqc.Group1_C2.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C2 threads: 5 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group1_C2 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group1_C2 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_C2/Group1_C2_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_fastqc.Group1_C2.txt 2>&1 [Tue Nov 19 05:01:22 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Tue Nov 19 04:59:24 2024] rule rule_2_cutadapt: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_C2/Group1_C2.R1.combined.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_C2/Group1_C2_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/2_cutadapt.Group1_C2.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C2 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -j 4 --times 2 -u 1 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_C2/Group1_C2_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_C2/Group1_C2.R1.combined.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_C2.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/2_cutadapt.Group1_C2.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_C2/Group1_C2_R1.fastq.gz.deleted [Tue Nov 19 04:59:59 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1155, disk_mb=1155, mem_mb_per_thread=400, mem_mb_total=200 Select jobs to execute... [Tue Nov 19 04:46:30 2024] rule rule_1_combined_fastq: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group1_C2/Group1_C2_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group1_C2/Group1_C2_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_C2/Group1_C2.R1.combined.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_C2/Group1_C2.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/1_combined_fastq.Group1_C2.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C2 resources: mem_mb=1155, disk_mb=1155, tmpdir=/tmp, mem_mb_per_thread=400, mem_mb_total=200 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/ExtractBCSR.py --fastqIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group1_C2/Group1_C2_R1.fastq.gz --fastqUMI /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group1_C2/Group1_C2_R2.fastq.gz --fastqOut /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_C2/Group1_C2.R1.combined.fastq.gz --bcHistFileName /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_C2/Group1_C2.umi_frequencies.csv > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_C2/Group1_C2.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/1_combined_fastq.Group1_C2.txt [Tue Nov 19 04:58:55 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1048, disk_mb=1048, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Tue Nov 19 05:24:29 2024] rule rule_3_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_C1/Group2_C1_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group2_C1/Group2_C1_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_fastqc.Group2_C1.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C1 threads: 5 resources: mem_mb=1048, disk_mb=1048, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group2_C1 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group2_C1 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_C1/Group2_C1_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_fastqc.Group2_C1.txt 2>&1 [Tue Nov 19 05:25:17 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1025, disk_mb=1025, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Tue Nov 19 05:04:04 2024] rule rule_2_cutadapt: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_C1/Group2_C1.R1.combined.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_C1/Group2_C1_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/2_cutadapt.Group2_C1.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C1 threads: 4 resources: mem_mb=1025, disk_mb=1025, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -j 4 --times 2 -u 1 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_C1/Group2_C1_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_C1/Group2_C1.R1.combined.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_C1.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/2_cutadapt.Group2_C1.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_C1/Group2_C1_R1.fastq.gz.deleted [Tue Nov 19 05:04:41 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1315, disk_mb=1315, mem_mb_per_thread=400, mem_mb_total=200 Select jobs to execute... [Tue Nov 19 04:46:24 2024] rule rule_1_combined_fastq: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group2_C1/Group2_C1_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group2_C1/Group2_C1_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_C1/Group2_C1.R1.combined.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_C1/Group2_C1.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/1_combined_fastq.Group2_C1.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C1 resources: mem_mb=1315, disk_mb=1315, tmpdir=/tmp, mem_mb_per_thread=400, mem_mb_total=200 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/ExtractBCSR.py --fastqIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group2_C1/Group2_C1_R1.fastq.gz --fastqUMI /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group2_C1/Group2_C1_R2.fastq.gz --fastqOut /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_C1/Group2_C1.R1.combined.fastq.gz --bcHistFileName /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_C1/Group2_C1.umi_frequencies.csv > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_C1/Group2_C1.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/1_combined_fastq.Group2_C1.txt [Tue Nov 19 05:02:49 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Tue Nov 19 04:59:12 2024] rule rule_3_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_C2/Group2_C2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group2_C2/Group2_C2_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_fastqc.Group2_C2.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C2 threads: 5 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group2_C2 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group2_C2 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_C2/Group2_C2_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_fastqc.Group2_C2.txt 2>&1 [Tue Nov 19 04:59:41 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Tue Nov 19 04:56:21 2024] rule rule_2_cutadapt: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_C2/Group2_C2.R1.combined.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_C2/Group2_C2_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/2_cutadapt.Group2_C2.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C2 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -j 4 --times 2 -u 1 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_C2/Group2_C2_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_C2/Group2_C2.R1.combined.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_C2.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/2_cutadapt.Group2_C2.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_C2/Group2_C2_R1.fastq.gz.deleted [Tue Nov 19 04:56:50 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=400, mem_mb_total=200 Select jobs to execute... [Tue Nov 19 04:46:24 2024] rule rule_1_combined_fastq: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group2_C2/Group2_C2_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group2_C2/Group2_C2_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_C2/Group2_C2.R1.combined.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_C2/Group2_C2.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/1_combined_fastq.Group2_C2.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=400, mem_mb_total=200 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/ExtractBCSR.py --fastqIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group2_C2/Group2_C2_R1.fastq.gz --fastqUMI /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group2_C2/Group2_C2_R2.fastq.gz --fastqOut /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_C2/Group2_C2.R1.combined.fastq.gz --bcHistFileName /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_C2/Group2_C2.umi_frequencies.csv > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_C2/Group2_C2.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/1_combined_fastq.Group2_C2.txt [Tue Nov 19 04:56:12 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=8200, disk_mb=8200, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:57:46 2024] rule rule_ngsplot: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/multiQC/multiqc_report.html, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group1_LPS1.deDup_counts.corrected.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group1_LPS2.deDup_counts.corrected.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group2_LPS1.deDup_counts.corrected.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group2_LPS2.deDup_counts.corrected.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group1_C1.deDup_counts.corrected.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group1_C2.deDup_counts.corrected.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group2_C1.deDup_counts.corrected.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group2_C2.deDup_counts.corrected.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS1Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS2Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS1Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS2Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C1Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C2Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C1Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C2Aligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/10_reports/ngsplotOut.avgprof.pdf log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/10_reports.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/ngsplot.txt jobid: 0 reason: Forced execution threads: 20 resources: mem_mb=8200, disk_mb=8200, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 [Tue Nov 19 06:04:37 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=1000, mem_mb_total=1000 Select jobs to execute... [Tue Nov 19 05:39:58 2024] rule rule_3_multiQC: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group1_LPS1/Group1_LPS1_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group1_LPS2/Group1_LPS2_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group2_LPS1/Group2_LPS1_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group2_LPS2/Group2_LPS2_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group1_C1/Group1_C1_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group1_C2/Group1_C2_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group2_C1/Group2_C1_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group2_C2/Group2_C2_R1_fastqc/fastqc_data.txt output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/multiQC/multiqc_report.html log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_multiQC.txt jobid: 0 reason: Forced execution resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=1000, mem_mb_total=1000 /opt/miniconda3/envs/utap/bin/multiqc -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/multiQC /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc &>/home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_multiQC.txt [Tue Nov 19 05:40:10 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=150, mem_mb_total=150 Select jobs to execute... [Tue Nov 19 05:52:42 2024] rule rule_9_umi_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group1_LPS1.deDup_counts.txt output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group1_LPS1.deDup_counts.corrected.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/9_umi_counts.Group1_LPS1.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=150, mem_mb_total=150, runtime=02:30 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/CorrectCounts.py --inputCounts /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group1_LPS1.deDup_counts.txt --bcLength 8 --outputCounts /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group1_LPS1.deDup_counts.corrected.txt > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/9_umi_counts.Group1_LPS1.txt 2>&1 [Tue Nov 19 05:52:43 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=300, mem_mb_total=300 Select jobs to execute... [Tue Nov 19 05:49:25 2024] rule rule_8_dedup_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_LPS1.gene.MDunsorted.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group1_LPS1.deDup_counts.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=300, mem_mb_total=300, runtime=02:30 /opt/miniconda3/envs/utap/bin/samtools view -F 1024 /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_LPS1.gene.MDunsorted.bam | grep -v RX:Z:[ACTG]*N[ACTGN]* | cat /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS1.header.sam - | /opt/miniconda3/envs/utap/bin/htseq-count -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf 2>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group1_LPS1.deDup_counts.txt [Tue Nov 19 05:52:22 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Tue Nov 19 05:02:28 2024] rule rule_3_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_LPS1/Group1_LPS1_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group1_LPS1/Group1_LPS1_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_fastqc.Group1_LPS1.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS1 threads: 5 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group1_LPS1 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group1_LPS1 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_LPS1/Group1_LPS1_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_fastqc.Group1_LPS1.txt 2>&1 [Tue Nov 19 05:03:05 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=5000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:46:33 2024] rule rule_7_mark_dup: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS1.gene.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_LPS1.gene.MDunsorted.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_LPS1.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS1 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=5000, mem_mb_total=20000, runtime=02:30 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_LPS1_deDupMetrics /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS1.gene.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_LPS1.txt 2>&1 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MarkDuplicatesUMIbyGene.py --inputBam /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS1.gene.bam --outputBam /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_LPS1.gene.MDunsorted.bam --bcLength 8 --gtf /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf --outputMetricsDir /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_LPS1_deDupMetrics --outputPrefix dup_Group1_LPS1 --logFile /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_LPS1.txt >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_LPS1.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_LPS1.gene.MDunsorted.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_LPS1.txt 2>&1 [Tue Nov 19 05:49:08 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=5000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:33:57 2024] rule rule_6_count_reads: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_LPS1.UMI.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS1.gene.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS1.gene.bam.bai log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group1_LPS1.samtools_view.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group1_LPS1.htseq_count.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS1 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=5000, mem_mb_total=20000, runtime=02:30 /opt/miniconda3/envs/utap/bin/samtools view -H /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_LPS1.UMI.out.bam -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS1.header.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group1_LPS1.samtools_view.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools view -h /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_LPS1.UMI.out.bam | /opt/miniconda3/envs/utap/bin/htseq-count -o /dev/fd/3 -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS1_counts.txt | /opt/miniconda3/envs/utap/bin/samtools view -Sb - > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS1.gene.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS1.gene.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group1_LPS1.samtools_view.txt 2>&1 touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS1.gene.bam.deleted touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS1.gene.bam.bai.deleted 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 412669 GFF lines processed. 100000 alignment records processed. 200000 alignment records processed. 300000 alignment records processed. 400000 alignment records processed. 500000 alignment records processed. 600000 alignment records processed. 700000 alignment records processed. 800000 alignment records processed. 900000 alignment records processed. 1000000 alignment records processed. 1100000 alignment records processed. 1200000 alignment records processed. 1300000 alignment records processed. 1400000 alignment records processed. 1500000 alignment records processed. 1600000 alignment records processed. 1700000 alignment records processed. 1800000 alignment records processed. 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7300000 alignment records processed. 7400000 alignment records processed. 7500000 alignment records processed. 7600000 alignment records processed. 7700000 alignment records processed. 7800000 alignment records processed. 7900000 alignment records processed. 8000000 alignment records processed. 8100000 alignment records processed. 8200000 alignment records processed. 8300000 alignment records processed. 8400000 alignment records processed. 8500000 alignment records processed. 8600000 alignment records processed. 8700000 alignment records processed. 8800000 alignment records processed. 8900000 alignment records processed. 9000000 alignment records processed. 9100000 alignment records processed. 9200000 alignment records processed. 9300000 alignment records processed. 9400000 alignment records processed. 9500000 alignment records processed. 9600000 alignment records processed. 9700000 alignment records processed. 9800000 alignment records processed. 9824343 alignment records processed. [Tue Nov 19 05:46:09 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=200, mem_mb_total=200 Select jobs to execute... [Tue Nov 19 05:32:22 2024] rule rule_5_move_umi: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS1Aligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_LPS1.UMI.out.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/5_move_umi.Group1_LPS1.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=200, mem_mb_total=200, runtime=02:30 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MoveBC.py --bamIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS1Aligned.sortedByCoord.out.bam --bamOut /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_LPS1.UMI.out.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/5_move_umi.Group1_LPS1.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_LPS1.UMI.out.bam.deleted [Tue Nov 19 05:33:43 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:30:06 2024] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_LPS1/Group1_LPS1_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS1Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS1Aligned.sortedByCoord.out.bam.bai log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/4_mapping.Group1_LPS1.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS1 threads: 20 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --genomeDir /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/STAR_v2.7.10a_index/ --readFilesIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_LPS1/Group1_LPS1_R1.fastq.gz --readFilesCommand zcat --alignEndsType EndToEnd --runThreadN 20 --genomeLoad NoSharedMemory --outFilterMismatchNoverLmax 0.05 --outSAMstrandField intronMotif --twopassMode Basic --outSAMtype BAM SortedByCoordinate --alignSoftClipAtReferenceEnds No --outFileNamePrefix /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS1 --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/4_mapping.Group1_LPS1.txt 2>&1; /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS1Aligned.sortedByCoord.out.bam touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS1Aligned.sortedByCoord.out.bam.deleted touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS1Aligned.sortedByCoord.out.bam.bai.deleted [Tue Nov 19 05:31:56 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=150, mem_mb_total=150 Select jobs to execute... [Tue Nov 19 05:53:49 2024] rule rule_9_umi_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group1_LPS2.deDup_counts.txt output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group1_LPS2.deDup_counts.corrected.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/9_umi_counts.Group1_LPS2.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=150, mem_mb_total=150, runtime=02:30 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/CorrectCounts.py --inputCounts /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group1_LPS2.deDup_counts.txt --bcLength 8 --outputCounts /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group1_LPS2.deDup_counts.corrected.txt > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/9_umi_counts.Group1_LPS2.txt 2>&1 [Tue Nov 19 05:53:50 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=300, mem_mb_total=300 Select jobs to execute... [Tue Nov 19 05:46:30 2024] rule rule_8_dedup_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_LPS2.gene.MDunsorted.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group1_LPS2.deDup_counts.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=300, mem_mb_total=300, runtime=02:30 /opt/miniconda3/envs/utap/bin/samtools view -F 1024 /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_LPS2.gene.MDunsorted.bam | grep -v RX:Z:[ACTG]*N[ACTGN]* | cat /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS2.header.sam - | /opt/miniconda3/envs/utap/bin/htseq-count -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf 2>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group1_LPS2.deDup_counts.txt [Tue Nov 19 05:53:26 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=5000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:44:15 2024] rule rule_7_mark_dup: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS2.gene.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_LPS2.gene.MDunsorted.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_LPS2.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS2 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=5000, mem_mb_total=20000, runtime=02:30 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_LPS2_deDupMetrics /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS2.gene.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_LPS2.txt 2>&1 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MarkDuplicatesUMIbyGene.py --inputBam /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS2.gene.bam --outputBam /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_LPS2.gene.MDunsorted.bam --bcLength 8 --gtf /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf --outputMetricsDir /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_LPS2_deDupMetrics --outputPrefix dup_Group1_LPS2 --logFile /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_LPS2.txt >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_LPS2.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_LPS2.gene.MDunsorted.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_LPS2.txt 2>&1 [Tue Nov 19 05:46:08 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=5000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:35:56 2024] rule rule_6_count_reads: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_LPS2.UMI.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS2.gene.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS2.gene.bam.bai log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group1_LPS2.samtools_view.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group1_LPS2.htseq_count.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS2 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=5000, mem_mb_total=20000, runtime=02:30 /opt/miniconda3/envs/utap/bin/samtools view -H /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_LPS2.UMI.out.bam -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS2.header.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group1_LPS2.samtools_view.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools view -h /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_LPS2.UMI.out.bam | /opt/miniconda3/envs/utap/bin/htseq-count -o /dev/fd/3 -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS2_counts.txt | /opt/miniconda3/envs/utap/bin/samtools view -Sb - > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS2.gene.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS2.gene.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group1_LPS2.samtools_view.txt 2>&1 touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS2.gene.bam.deleted touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_LPS2.gene.bam.bai.deleted 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 412669 GFF lines processed. 100000 alignment records processed. 200000 alignment records processed. 300000 alignment records processed. 400000 alignment records processed. 500000 alignment records processed. 600000 alignment records processed. 700000 alignment records processed. 800000 alignment records processed. 900000 alignment records processed. 1000000 alignment records processed. 1100000 alignment records processed. 1200000 alignment records processed. 1300000 alignment records processed. 1400000 alignment records processed. 1500000 alignment records processed. 1600000 alignment records processed. 1700000 alignment records processed. 1800000 alignment records processed. 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[Tue Nov 19 05:44:03 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1072, disk_mb=1072, mem_mb_per_thread=200, mem_mb_total=200 Select jobs to execute... [Tue Nov 19 05:34:20 2024] rule rule_5_move_umi: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS2Aligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_LPS2.UMI.out.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/5_move_umi.Group1_LPS2.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS2 resources: mem_mb=1072, disk_mb=1072, tmpdir=/tmp, mem_mb_per_thread=200, mem_mb_total=200, runtime=02:30 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MoveBC.py --bamIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS2Aligned.sortedByCoord.out.bam --bamOut /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_LPS2.UMI.out.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/5_move_umi.Group1_LPS2.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_LPS2.UMI.out.bam.deleted [Tue Nov 19 05:35:36 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:32:02 2024] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_LPS2/Group1_LPS2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS2Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS2Aligned.sortedByCoord.out.bam.bai log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/4_mapping.Group1_LPS2.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS2 threads: 20 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --genomeDir /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/STAR_v2.7.10a_index/ --readFilesIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_LPS2/Group1_LPS2_R1.fastq.gz --readFilesCommand zcat --alignEndsType EndToEnd --runThreadN 20 --genomeLoad NoSharedMemory --outFilterMismatchNoverLmax 0.05 --outSAMstrandField intronMotif --twopassMode Basic --outSAMtype BAM SortedByCoordinate --alignSoftClipAtReferenceEnds No --outFileNamePrefix /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS2 --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/4_mapping.Group1_LPS2.txt 2>&1; /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS2Aligned.sortedByCoord.out.bam touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS2Aligned.sortedByCoord.out.bam.deleted touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_LPS2Aligned.sortedByCoord.out.bam.bai.deleted [Tue Nov 19 05:33:56 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Tue Nov 19 04:59:53 2024] rule rule_2_cutadapt: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_LPS1/Group1_LPS1.R1.combined.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_LPS1/Group1_LPS1_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/2_cutadapt.Group1_LPS1.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS1 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -j 4 --times 2 -u 1 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_LPS1/Group1_LPS1_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_LPS1/Group1_LPS1.R1.combined.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_LPS1.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/2_cutadapt.Group1_LPS1.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_LPS1/Group1_LPS1_R1.fastq.gz.deleted [Tue Nov 19 05:00:24 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=150, mem_mb_total=150 Select jobs to execute... [Tue Nov 19 05:40:42 2024] rule rule_9_umi_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group2_LPS1.deDup_counts.txt output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group2_LPS1.deDup_counts.corrected.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/9_umi_counts.Group2_LPS1.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=150, mem_mb_total=150, runtime=02:30 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/CorrectCounts.py --inputCounts /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group2_LPS1.deDup_counts.txt --bcLength 8 --outputCounts /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group2_LPS1.deDup_counts.corrected.txt > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/9_umi_counts.Group2_LPS1.txt 2>&1 [Tue Nov 19 05:40:43 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=300, mem_mb_total=300 Select jobs to execute... [Tue Nov 19 05:38:18 2024] rule rule_8_dedup_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_LPS1.gene.MDunsorted.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group2_LPS1.deDup_counts.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=300, mem_mb_total=300, runtime=02:30 /opt/miniconda3/envs/utap/bin/samtools view -F 1024 /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_LPS1.gene.MDunsorted.bam | grep -v RX:Z:[ACTG]*N[ACTGN]* | cat /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS1.header.sam - | /opt/miniconda3/envs/utap/bin/htseq-count -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf 2>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group2_LPS1.deDup_counts.txt [Tue Nov 19 05:40:26 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=5000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:36:19 2024] rule rule_7_mark_dup: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS1.gene.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_LPS1.gene.MDunsorted.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_LPS1.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS1 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=5000, mem_mb_total=20000, runtime=02:30 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_LPS1_deDupMetrics /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS1.gene.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_LPS1.txt 2>&1 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MarkDuplicatesUMIbyGene.py --inputBam /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS1.gene.bam --outputBam /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_LPS1.gene.MDunsorted.bam --bcLength 8 --gtf /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf --outputMetricsDir /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_LPS1_deDupMetrics --outputPrefix dup_Group2_LPS1 --logFile /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_LPS1.txt >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_LPS1.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_LPS1.gene.MDunsorted.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_LPS1.txt 2>&1 [Tue Nov 19 05:37:58 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=5000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:27:44 2024] rule rule_6_count_reads: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_LPS1.UMI.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS1.gene.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS1.gene.bam.bai log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group2_LPS1.samtools_view.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group2_LPS1.htseq_count.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS1 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=5000, mem_mb_total=20000, runtime=02:30 /opt/miniconda3/envs/utap/bin/samtools view -H /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_LPS1.UMI.out.bam -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS1.header.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group2_LPS1.samtools_view.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools view -h /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_LPS1.UMI.out.bam | /opt/miniconda3/envs/utap/bin/htseq-count -o /dev/fd/3 -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS1_counts.txt | /opt/miniconda3/envs/utap/bin/samtools view -Sb - > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS1.gene.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS1.gene.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group2_LPS1.samtools_view.txt 2>&1 touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS1.gene.bam.deleted touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS1.gene.bam.bai.deleted 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 412669 GFF lines processed. 100000 alignment records processed. 200000 alignment records processed. 300000 alignment records processed. 400000 alignment records processed. 500000 alignment records processed. 600000 alignment records processed. 700000 alignment records processed. 800000 alignment records processed. 900000 alignment records processed. 1000000 alignment records processed. 1100000 alignment records processed. 1200000 alignment records processed. 1300000 alignment records processed. 1400000 alignment records processed. 1500000 alignment records processed. 1600000 alignment records processed. 1700000 alignment records processed. 1800000 alignment records processed. 1900000 alignment records processed. 2000000 alignment records processed. 2100000 alignment records processed. 2200000 alignment records processed. 2300000 alignment records processed. 2400000 alignment records processed. 2500000 alignment records processed. 2600000 alignment records processed. 2700000 alignment records processed. 2800000 alignment records processed. 2900000 alignment records processed. 3000000 alignment records processed. 3100000 alignment records processed. 3200000 alignment records processed. 3300000 alignment records processed. 3400000 alignment records processed. 3500000 alignment records processed. 3600000 alignment records processed. 3700000 alignment records processed. 3800000 alignment records processed. 3900000 alignment records processed. 4000000 alignment records processed. 4100000 alignment records processed. 4200000 alignment records processed. 4300000 alignment records processed. 4400000 alignment records processed. 4500000 alignment records processed. 4600000 alignment records processed. 4700000 alignment records processed. 4800000 alignment records processed. 4900000 alignment records processed. 5000000 alignment records processed. 5100000 alignment records processed. 5200000 alignment records processed. 5300000 alignment records processed. 5400000 alignment records processed. 5500000 alignment records processed. 5600000 alignment records processed. 5700000 alignment records processed. 5800000 alignment records processed. 5900000 alignment records processed. 6000000 alignment records processed. 6100000 alignment records processed. 6200000 alignment records processed. 6300000 alignment records processed. 6400000 alignment records processed. 6500000 alignment records processed. 6600000 alignment records processed. 6700000 alignment records processed. 6800000 alignment records processed. 6900000 alignment records processed. 7000000 alignment records processed. 7100000 alignment records processed. 7200000 alignment records processed. 7300000 alignment records processed. 7400000 alignment records processed. 7500000 alignment records processed. 7600000 alignment records processed. 7700000 alignment records processed. 7800000 alignment records processed. 7900000 alignment records processed. 8000000 alignment records processed. 8100000 alignment records processed. 8200000 alignment records processed. 8300000 alignment records processed. 8400000 alignment records processed. 8500000 alignment records processed. 8593639 alignment records processed. [Tue Nov 19 05:36:04 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=200, mem_mb_total=200 Select jobs to execute... [Tue Nov 19 05:26:11 2024] rule rule_5_move_umi: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS1Aligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_LPS1.UMI.out.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/5_move_umi.Group2_LPS1.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=200, mem_mb_total=200, runtime=02:30 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MoveBC.py --bamIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS1Aligned.sortedByCoord.out.bam --bamOut /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_LPS1.UMI.out.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/5_move_umi.Group2_LPS1.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_LPS1.UMI.out.bam.deleted [Tue Nov 19 05:27:23 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:20:37 2024] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_LPS1/Group2_LPS1_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS1Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS1Aligned.sortedByCoord.out.bam.bai log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/4_mapping.Group2_LPS1.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS1 threads: 20 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --genomeDir /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/STAR_v2.7.10a_index/ --readFilesIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_LPS1/Group2_LPS1_R1.fastq.gz --readFilesCommand zcat --alignEndsType EndToEnd --runThreadN 20 --genomeLoad NoSharedMemory --outFilterMismatchNoverLmax 0.05 --outSAMstrandField intronMotif --twopassMode Basic --outSAMtype BAM SortedByCoordinate --alignSoftClipAtReferenceEnds No --outFileNamePrefix /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS1 --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/4_mapping.Group2_LPS1.txt 2>&1; /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS1Aligned.sortedByCoord.out.bam touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS1Aligned.sortedByCoord.out.bam.deleted touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS1Aligned.sortedByCoord.out.bam.bai.deleted [Tue Nov 19 05:24:06 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=150, mem_mb_total=150 Select jobs to execute... [Tue Nov 19 05:47:57 2024] rule rule_9_umi_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group2_LPS2.deDup_counts.txt output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group2_LPS2.deDup_counts.corrected.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/9_umi_counts.Group2_LPS2.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=150, mem_mb_total=150, runtime=02:30 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/CorrectCounts.py --inputCounts /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group2_LPS2.deDup_counts.txt --bcLength 8 --outputCounts /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group2_LPS2.deDup_counts.corrected.txt > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/9_umi_counts.Group2_LPS2.txt 2>&1 [Tue Nov 19 05:47:59 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=300, mem_mb_total=300 Select jobs to execute... [Tue Nov 19 05:41:51 2024] rule rule_8_dedup_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_LPS2.gene.MDunsorted.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group2_LPS2.deDup_counts.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=300, mem_mb_total=300, runtime=02:30 /opt/miniconda3/envs/utap/bin/samtools view -F 1024 /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_LPS2.gene.MDunsorted.bam | grep -v RX:Z:[ACTG]*N[ACTGN]* | cat /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS2.header.sam - | /opt/miniconda3/envs/utap/bin/htseq-count -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf 2>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group2_LPS2.deDup_counts.txt [Tue Nov 19 05:47:22 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=5000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:39:12 2024] rule rule_7_mark_dup: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS2.gene.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_LPS2.gene.MDunsorted.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_LPS2.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS2 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=5000, mem_mb_total=20000, runtime=02:30 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_LPS2_deDupMetrics /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS2.gene.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_LPS2.txt 2>&1 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MarkDuplicatesUMIbyGene.py --inputBam /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS2.gene.bam --outputBam /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_LPS2.gene.MDunsorted.bam --bcLength 8 --gtf /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf --outputMetricsDir /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_LPS2_deDupMetrics --outputPrefix dup_Group2_LPS2 --logFile /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_LPS2.txt >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_LPS2.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_LPS2.gene.MDunsorted.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_LPS2.txt 2>&1 [Tue Nov 19 05:41:22 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=5000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:29:45 2024] rule rule_6_count_reads: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_LPS2.UMI.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS2.gene.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS2.gene.bam.bai log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group2_LPS2.samtools_view.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group2_LPS2.htseq_count.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS2 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=5000, mem_mb_total=20000, runtime=02:30 /opt/miniconda3/envs/utap/bin/samtools view -H /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_LPS2.UMI.out.bam -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS2.header.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group2_LPS2.samtools_view.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools view -h /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_LPS2.UMI.out.bam | /opt/miniconda3/envs/utap/bin/htseq-count -o /dev/fd/3 -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS2_counts.txt | /opt/miniconda3/envs/utap/bin/samtools view -Sb - > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS2.gene.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS2.gene.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group2_LPS2.samtools_view.txt 2>&1 touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS2.gene.bam.deleted touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_LPS2.gene.bam.bai.deleted 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 412669 GFF lines processed. 100000 alignment records processed. 200000 alignment records processed. 300000 alignment records processed. 400000 alignment records processed. 500000 alignment records processed. 600000 alignment records processed. 700000 alignment records processed. 800000 alignment records processed. 900000 alignment records processed. 1000000 alignment records processed. 1100000 alignment records processed. 1200000 alignment records processed. 1300000 alignment records processed. 1400000 alignment records processed. 1500000 alignment records processed. 1600000 alignment records processed. 1700000 alignment records processed. 1800000 alignment records processed. 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7300000 alignment records processed. 7400000 alignment records processed. 7500000 alignment records processed. 7600000 alignment records processed. 7700000 alignment records processed. 7800000 alignment records processed. 7900000 alignment records processed. 8000000 alignment records processed. 8100000 alignment records processed. 8200000 alignment records processed. 8300000 alignment records processed. 8400000 alignment records processed. 8500000 alignment records processed. 8600000 alignment records processed. 8700000 alignment records processed. 8800000 alignment records processed. 8900000 alignment records processed. 9000000 alignment records processed. 9100000 alignment records processed. 9200000 alignment records processed. 9300000 alignment records processed. 9400000 alignment records processed. 9480088 alignment records processed. [Tue Nov 19 05:38:46 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1064, disk_mb=1064, mem_mb_per_thread=400, mem_mb_total=200 Select jobs to execute... [Tue Nov 19 04:46:26 2024] rule rule_1_combined_fastq: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group1_LPS1/Group1_LPS1_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group1_LPS1/Group1_LPS1_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_LPS1/Group1_LPS1.R1.combined.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_LPS1/Group1_LPS1.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/1_combined_fastq.Group1_LPS1.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS1 resources: mem_mb=1064, disk_mb=1064, tmpdir=/tmp, mem_mb_per_thread=400, mem_mb_total=200 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/ExtractBCSR.py --fastqIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group1_LPS1/Group1_LPS1_R1.fastq.gz --fastqUMI /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group1_LPS1/Group1_LPS1_R2.fastq.gz --fastqOut /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_LPS1/Group1_LPS1.R1.combined.fastq.gz --bcHistFileName /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_LPS1/Group1_LPS1.umi_frequencies.csv > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_LPS1/Group1_LPS1.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/1_combined_fastq.Group1_LPS1.txt [Tue Nov 19 04:59:03 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=200, mem_mb_total=200 Select jobs to execute... [Tue Nov 19 05:28:11 2024] rule rule_5_move_umi: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS2Aligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_LPS2.UMI.out.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/5_move_umi.Group2_LPS2.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=200, mem_mb_total=200, runtime=02:30 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MoveBC.py --bamIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS2Aligned.sortedByCoord.out.bam --bamOut /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_LPS2.UMI.out.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/5_move_umi.Group2_LPS2.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_LPS2.UMI.out.bam.deleted [Tue Nov 19 05:29:35 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:26:07 2024] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_LPS2/Group2_LPS2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS2Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS2Aligned.sortedByCoord.out.bam.bai log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/4_mapping.Group2_LPS2.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS2 threads: 20 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --genomeDir /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/STAR_v2.7.10a_index/ --readFilesIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_LPS2/Group2_LPS2_R1.fastq.gz --readFilesCommand zcat --alignEndsType EndToEnd --runThreadN 20 --genomeLoad NoSharedMemory --outFilterMismatchNoverLmax 0.05 --outSAMstrandField intronMotif --twopassMode Basic --outSAMtype BAM SortedByCoordinate --alignSoftClipAtReferenceEnds No --outFileNamePrefix /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS2 --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/4_mapping.Group2_LPS2.txt 2>&1; /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS2Aligned.sortedByCoord.out.bam touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS2Aligned.sortedByCoord.out.bam.deleted touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_LPS2Aligned.sortedByCoord.out.bam.bai.deleted [Tue Nov 19 05:28:02 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=150, mem_mb_total=150 Select jobs to execute... [Tue Nov 19 05:53:38 2024] rule rule_9_umi_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group1_C1.deDup_counts.txt output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group1_C1.deDup_counts.corrected.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/9_umi_counts.Group1_C1.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=150, mem_mb_total=150, runtime=02:30 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/CorrectCounts.py --inputCounts /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group1_C1.deDup_counts.txt --bcLength 8 --outputCounts /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group1_C1.deDup_counts.corrected.txt > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/9_umi_counts.Group1_C1.txt 2>&1 [Tue Nov 19 05:53:39 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=300, mem_mb_total=300 Select jobs to execute... [Tue Nov 19 05:50:36 2024] rule rule_8_dedup_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_C1.gene.MDunsorted.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group1_C1.deDup_counts.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=300, mem_mb_total=300, runtime=02:30 /opt/miniconda3/envs/utap/bin/samtools view -F 1024 /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_C1.gene.MDunsorted.bam | grep -v RX:Z:[ACTG]*N[ACTGN]* | cat /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C1.header.sam - | /opt/miniconda3/envs/utap/bin/htseq-count -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf 2>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group1_C1.deDup_counts.txt [Tue Nov 19 05:53:25 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=5000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:48:04 2024] rule rule_7_mark_dup: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C1.gene.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_C1.gene.MDunsorted.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_C1.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C1 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=5000, mem_mb_total=20000, runtime=02:30 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_C1_deDupMetrics /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C1.gene.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_C1.txt 2>&1 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MarkDuplicatesUMIbyGene.py --inputBam /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C1.gene.bam --outputBam /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_C1.gene.MDunsorted.bam --bcLength 8 --gtf /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf --outputMetricsDir /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_C1_deDupMetrics --outputPrefix dup_Group1_C1 --logFile /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_C1.txt >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_C1.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_C1.gene.MDunsorted.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_C1.txt 2>&1 [Tue Nov 19 05:50:16 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=5000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:38:21 2024] rule rule_6_count_reads: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_C1.UMI.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C1.gene.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C1.gene.bam.bai log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group1_C1.samtools_view.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group1_C1.htseq_count.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C1 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=5000, mem_mb_total=20000, runtime=02:30 /opt/miniconda3/envs/utap/bin/samtools view -H /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_C1.UMI.out.bam -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C1.header.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group1_C1.samtools_view.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools view -h /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_C1.UMI.out.bam | /opt/miniconda3/envs/utap/bin/htseq-count -o /dev/fd/3 -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C1_counts.txt | /opt/miniconda3/envs/utap/bin/samtools view -Sb - > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C1.gene.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C1.gene.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group1_C1.samtools_view.txt 2>&1 touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C1.gene.bam.deleted touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C1.gene.bam.bai.deleted 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 412669 GFF lines processed. 100000 alignment records processed. 200000 alignment records processed. 300000 alignment records processed. 400000 alignment records processed. 500000 alignment records processed. 600000 alignment records processed. 700000 alignment records processed. 800000 alignment records processed. 900000 alignment records processed. 1000000 alignment records processed. 1100000 alignment records processed. 1200000 alignment records processed. 1300000 alignment records processed. 1400000 alignment records processed. 1500000 alignment records processed. 1600000 alignment records processed. 1700000 alignment records processed. 1800000 alignment records processed. 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10000000 alignment records processed. 10100000 alignment records processed. 10200000 alignment records processed. 10300000 alignment records processed. 10400000 alignment records processed. 10500000 alignment records processed. 10600000 alignment records processed. 10700000 alignment records processed. 10800000 alignment records processed. 10900000 alignment records processed. 11000000 alignment records processed. 11100000 alignment records processed. 11200000 alignment records processed. 11300000 alignment records processed. 11400000 alignment records processed. 11500000 alignment records processed. 11600000 alignment records processed. 11700000 alignment records processed. 11800000 alignment records processed. 11900000 alignment records processed. 12000000 alignment records processed. 12100000 alignment records processed. 12200000 alignment records processed. 12300000 alignment records processed. 12400000 alignment records processed. 12430659 alignment records processed. [Tue Nov 19 05:47:30 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1215, disk_mb=1215, mem_mb_per_thread=200, mem_mb_total=200 Select jobs to execute... [Tue Nov 19 05:36:19 2024] rule rule_5_move_umi: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C1Aligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_C1.UMI.out.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/5_move_umi.Group1_C1.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C1 resources: mem_mb=1215, disk_mb=1215, tmpdir=/tmp, mem_mb_per_thread=200, mem_mb_total=200, runtime=02:30 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MoveBC.py --bamIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C1Aligned.sortedByCoord.out.bam --bamOut /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_C1.UMI.out.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/5_move_umi.Group1_C1.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_C1.UMI.out.bam.deleted [Tue Nov 19 05:38:08 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1033, disk_mb=1033, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:34:01 2024] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_C1/Group1_C1_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C1Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C1Aligned.sortedByCoord.out.bam.bai log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/4_mapping.Group1_C1.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C1 threads: 20 resources: mem_mb=1033, disk_mb=1033, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --genomeDir /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/STAR_v2.7.10a_index/ --readFilesIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_C1/Group1_C1_R1.fastq.gz --readFilesCommand zcat --alignEndsType EndToEnd --runThreadN 20 --genomeLoad NoSharedMemory --outFilterMismatchNoverLmax 0.05 --outSAMstrandField intronMotif --twopassMode Basic --outSAMtype BAM SortedByCoordinate --alignSoftClipAtReferenceEnds No --outFileNamePrefix /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C1 --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/4_mapping.Group1_C1.txt 2>&1; /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C1Aligned.sortedByCoord.out.bam touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C1Aligned.sortedByCoord.out.bam.deleted touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C1Aligned.sortedByCoord.out.bam.bai.deleted [Tue Nov 19 05:35:57 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=150, mem_mb_total=150 Select jobs to execute... [Tue Nov 19 05:47:22 2024] rule rule_9_umi_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group1_C2.deDup_counts.txt output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group1_C2.deDup_counts.corrected.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/9_umi_counts.Group1_C2.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=150, mem_mb_total=150, runtime=02:30 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/CorrectCounts.py --inputCounts /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group1_C2.deDup_counts.txt --bcLength 8 --outputCounts /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group1_C2.deDup_counts.corrected.txt > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/9_umi_counts.Group1_C2.txt 2>&1 [Tue Nov 19 05:47:24 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=300, mem_mb_total=300 Select jobs to execute... [Tue Nov 19 05:44:01 2024] rule rule_8_dedup_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_C2.gene.MDunsorted.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group1_C2.deDup_counts.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=300, mem_mb_total=300, runtime=02:30 /opt/miniconda3/envs/utap/bin/samtools view -F 1024 /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_C2.gene.MDunsorted.bam | grep -v RX:Z:[ACTG]*N[ACTGN]* | cat /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C2.header.sam - | /opt/miniconda3/envs/utap/bin/htseq-count -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf 2>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group1_C2.deDup_counts.txt [Tue Nov 19 05:47:04 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Tue Nov 19 05:01:35 2024] rule rule_3_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_LPS2/Group1_LPS2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group1_LPS2/Group1_LPS2_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_fastqc.Group1_LPS2.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS2 threads: 5 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group1_LPS2 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group1_LPS2 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_LPS2/Group1_LPS2_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_fastqc.Group1_LPS2.txt 2>&1 [Tue Nov 19 05:02:14 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=5000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:41:35 2024] rule rule_7_mark_dup: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C2.gene.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_C2.gene.MDunsorted.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_C2.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C2 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=5000, mem_mb_total=20000, runtime=02:30 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_C2_deDupMetrics /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C2.gene.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_C2.txt 2>&1 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MarkDuplicatesUMIbyGene.py --inputBam /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C2.gene.bam --outputBam /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_C2.gene.MDunsorted.bam --bcLength 8 --gtf /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf --outputMetricsDir /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_C2_deDupMetrics --outputPrefix dup_Group1_C2 --logFile /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_C2.txt >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_C2.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group1_C2.gene.MDunsorted.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group1_C2.txt 2>&1 [Tue Nov 19 05:43:49 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=5000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:31:44 2024] rule rule_6_count_reads: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_C2.UMI.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C2.gene.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C2.gene.bam.bai log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group1_C2.samtools_view.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group1_C2.htseq_count.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C2 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=5000, mem_mb_total=20000, runtime=02:30 /opt/miniconda3/envs/utap/bin/samtools view -H /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_C2.UMI.out.bam -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C2.header.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group1_C2.samtools_view.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools view -h /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_C2.UMI.out.bam | /opt/miniconda3/envs/utap/bin/htseq-count -o /dev/fd/3 -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C2_counts.txt | /opt/miniconda3/envs/utap/bin/samtools view -Sb - > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C2.gene.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C2.gene.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group1_C2.samtools_view.txt 2>&1 touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C2.gene.bam.deleted touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group1_C2.gene.bam.bai.deleted 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 412669 GFF lines processed. 100000 alignment records processed. 200000 alignment records processed. 300000 alignment records processed. 400000 alignment records processed. 500000 alignment records processed. 600000 alignment records processed. 700000 alignment records processed. 800000 alignment records processed. 900000 alignment records processed. 1000000 alignment records processed. 1100000 alignment records processed. 1200000 alignment records processed. 1300000 alignment records processed. 1400000 alignment records processed. 1500000 alignment records processed. 1600000 alignment records processed. 1700000 alignment records processed. 1800000 alignment records processed. 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4600000 alignment records processed. 4700000 alignment records processed. 4800000 alignment records processed. 4900000 alignment records processed. 5000000 alignment records processed. 5100000 alignment records processed. 5200000 alignment records processed. 5300000 alignment records processed. 5400000 alignment records processed. 5500000 alignment records processed. 5600000 alignment records processed. 5700000 alignment records processed. 5800000 alignment records processed. 5900000 alignment records processed. 6000000 alignment records processed. 6100000 alignment records processed. 6200000 alignment records processed. 6300000 alignment records processed. 6400000 alignment records processed. 6500000 alignment records processed. 6600000 alignment records processed. 6700000 alignment records processed. 6800000 alignment records processed. 6900000 alignment records processed. 7000000 alignment records processed. 7100000 alignment records processed. 7200000 alignment records processed. 7300000 alignment records processed. 7400000 alignment records processed. 7500000 alignment records processed. 7600000 alignment records processed. 7700000 alignment records processed. 7800000 alignment records processed. 7900000 alignment records processed. 8000000 alignment records processed. 8100000 alignment records processed. 8200000 alignment records processed. 8300000 alignment records processed. 8400000 alignment records processed. 8500000 alignment records processed. 8600000 alignment records processed. 8700000 alignment records processed. 8800000 alignment records processed. 8900000 alignment records processed. 9000000 alignment records processed. 9100000 alignment records processed. 9200000 alignment records processed. 9300000 alignment records processed. 9400000 alignment records processed. 9500000 alignment records processed. 9600000 alignment records processed. 9700000 alignment records processed. 9800000 alignment records processed. 9900000 alignment records processed. 10000000 alignment records processed. 10100000 alignment records processed. 10200000 alignment records processed. 10300000 alignment records processed. 10400000 alignment records processed. 10500000 alignment records processed. 10600000 alignment records processed. 10700000 alignment records processed. 10800000 alignment records processed. 10900000 alignment records processed. 11000000 alignment records processed. 11100000 alignment records processed. 11200000 alignment records processed. 11300000 alignment records processed. 11393880 alignment records processed. [Tue Nov 19 05:41:21 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1113, disk_mb=1113, mem_mb_per_thread=200, mem_mb_total=200 Select jobs to execute... [Tue Nov 19 05:30:10 2024] rule rule_5_move_umi: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C2Aligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_C2.UMI.out.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/5_move_umi.Group1_C2.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C2 resources: mem_mb=1113, disk_mb=1113, tmpdir=/tmp, mem_mb_per_thread=200, mem_mb_total=200, runtime=02:30 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MoveBC.py --bamIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C2Aligned.sortedByCoord.out.bam --bamOut /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_C2.UMI.out.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/5_move_umi.Group1_C2.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group1_C2.UMI.out.bam.deleted [Tue Nov 19 05:31:29 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:28:06 2024] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_C2/Group1_C2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C2Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C2Aligned.sortedByCoord.out.bam.bai log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/4_mapping.Group1_C2.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_C2 threads: 20 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --genomeDir /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/STAR_v2.7.10a_index/ --readFilesIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_C2/Group1_C2_R1.fastq.gz --readFilesCommand zcat --alignEndsType EndToEnd --runThreadN 20 --genomeLoad NoSharedMemory --outFilterMismatchNoverLmax 0.05 --outSAMstrandField intronMotif --twopassMode Basic --outSAMtype BAM SortedByCoordinate --alignSoftClipAtReferenceEnds No --outFileNamePrefix /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C2 --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/4_mapping.Group1_C2.txt 2>&1; /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C2Aligned.sortedByCoord.out.bam touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C2Aligned.sortedByCoord.out.bam.deleted touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group1_C2Aligned.sortedByCoord.out.bam.bai.deleted [Tue Nov 19 05:30:01 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=150, mem_mb_total=150 Select jobs to execute... [Tue Nov 19 05:56:06 2024] rule rule_9_umi_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group2_C1.deDup_counts.txt output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group2_C1.deDup_counts.corrected.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/9_umi_counts.Group2_C1.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=150, mem_mb_total=150, runtime=02:30 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/CorrectCounts.py --inputCounts /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group2_C1.deDup_counts.txt --bcLength 8 --outputCounts /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group2_C1.deDup_counts.corrected.txt > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/9_umi_counts.Group2_C1.txt 2>&1 [Tue Nov 19 05:56:07 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=300, mem_mb_total=300 Select jobs to execute... [Tue Nov 19 05:52:53 2024] rule rule_8_dedup_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_C1.gene.MDunsorted.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group2_C1.deDup_counts.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=300, mem_mb_total=300, runtime=02:30 /opt/miniconda3/envs/utap/bin/samtools view -F 1024 /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_C1.gene.MDunsorted.bam | grep -v RX:Z:[ACTG]*N[ACTGN]* | cat /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C1.header.sam - | /opt/miniconda3/envs/utap/bin/htseq-count -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf 2>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group2_C1.deDup_counts.txt [Tue Nov 19 05:55:48 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=5000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:50:11 2024] rule rule_7_mark_dup: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C1.gene.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_C1.gene.MDunsorted.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_C1.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C1 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=5000, mem_mb_total=20000, runtime=02:30 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_C1_deDupMetrics /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C1.gene.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_C1.txt 2>&1 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MarkDuplicatesUMIbyGene.py --inputBam /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C1.gene.bam --outputBam /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_C1.gene.MDunsorted.bam --bcLength 8 --gtf /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf --outputMetricsDir /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_C1_deDupMetrics --outputPrefix dup_Group2_C1 --logFile /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_C1.txt >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_C1.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_C1.gene.MDunsorted.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_C1.txt 2>&1 [Tue Nov 19 05:52:41 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=5000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:40:05 2024] rule rule_6_count_reads: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_C1.UMI.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C1.gene.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C1.gene.bam.bai log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group2_C1.samtools_view.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group2_C1.htseq_count.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C1 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=5000, mem_mb_total=20000, runtime=02:30 /opt/miniconda3/envs/utap/bin/samtools view -H /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_C1.UMI.out.bam -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C1.header.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group2_C1.samtools_view.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools view -h /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_C1.UMI.out.bam | /opt/miniconda3/envs/utap/bin/htseq-count -o /dev/fd/3 -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C1_counts.txt | /opt/miniconda3/envs/utap/bin/samtools view -Sb - > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C1.gene.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C1.gene.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group2_C1.samtools_view.txt 2>&1 touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C1.gene.bam.deleted touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C1.gene.bam.bai.deleted 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 412669 GFF lines processed. 100000 alignment records processed. 200000 alignment records processed. 300000 alignment records processed. 400000 alignment records processed. 500000 alignment records processed. 600000 alignment records processed. 700000 alignment records processed. 800000 alignment records processed. 900000 alignment records processed. 1000000 alignment records processed. 1100000 alignment records processed. 1200000 alignment records processed. 1300000 alignment records processed. 1400000 alignment records processed. 1500000 alignment records processed. 1600000 alignment records processed. 1700000 alignment records processed. 1800000 alignment records processed. 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[Tue Nov 19 05:49:56 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1228, disk_mb=1228, mem_mb_per_thread=200, mem_mb_total=200 Select jobs to execute... [Tue Nov 19 05:38:18 2024] rule rule_5_move_umi: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C1Aligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_C1.UMI.out.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/5_move_umi.Group2_C1.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C1 resources: mem_mb=1228, disk_mb=1228, tmpdir=/tmp, mem_mb_per_thread=200, mem_mb_total=200, runtime=02:30 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MoveBC.py --bamIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C1Aligned.sortedByCoord.out.bam --bamOut /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_C1.UMI.out.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/5_move_umi.Group2_C1.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_C1.UMI.out.bam.deleted [Tue Nov 19 05:39:48 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1048, disk_mb=1048, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:36:03 2024] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_C1/Group2_C1_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C1Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C1Aligned.sortedByCoord.out.bam.bai log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/4_mapping.Group2_C1.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C1 threads: 20 resources: mem_mb=1048, disk_mb=1048, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --genomeDir /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/STAR_v2.7.10a_index/ --readFilesIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_C1/Group2_C1_R1.fastq.gz --readFilesCommand zcat --alignEndsType EndToEnd --runThreadN 20 --genomeLoad NoSharedMemory --outFilterMismatchNoverLmax 0.05 --outSAMstrandField intronMotif --twopassMode Basic --outSAMtype BAM SortedByCoordinate --alignSoftClipAtReferenceEnds No --outFileNamePrefix /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C1 --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/4_mapping.Group2_C1.txt 2>&1; /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C1Aligned.sortedByCoord.out.bam touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C1Aligned.sortedByCoord.out.bam.deleted touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C1Aligned.sortedByCoord.out.bam.bai.deleted [Tue Nov 19 05:37:59 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Tue Nov 19 05:00:01 2024] rule rule_2_cutadapt: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_LPS2/Group1_LPS2.R1.combined.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_LPS2/Group1_LPS2_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/2_cutadapt.Group1_LPS2.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS2 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -j 4 --times 2 -u 1 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_LPS2/Group1_LPS2_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_LPS2/Group1_LPS2.R1.combined.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_LPS2.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/2_cutadapt.Group1_LPS2.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group1_LPS2/Group1_LPS2_R1.fastq.gz.deleted [Tue Nov 19 05:00:33 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=150, mem_mb_total=150 Select jobs to execute... [Tue Nov 19 05:39:16 2024] rule rule_9_umi_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group2_C2.deDup_counts.txt output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group2_C2.deDup_counts.corrected.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/9_umi_counts.Group2_C2.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=150, mem_mb_total=150, runtime=02:30 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/CorrectCounts.py --inputCounts /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group2_C2.deDup_counts.txt --bcLength 8 --outputCounts /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/9_umi_counts/Group2_C2.deDup_counts.corrected.txt > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/9_umi_counts.Group2_C2.txt 2>&1 [Tue Nov 19 05:39:18 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=300, mem_mb_total=300 Select jobs to execute... [Tue Nov 19 05:36:18 2024] rule rule_8_dedup_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_C2.gene.MDunsorted.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group2_C2.deDup_counts.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=300, mem_mb_total=300, runtime=02:30 /opt/miniconda3/envs/utap/bin/samtools view -F 1024 /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_C2.gene.MDunsorted.bam | grep -v RX:Z:[ACTG]*N[ACTGN]* | cat /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C2.header.sam - | /opt/miniconda3/envs/utap/bin/htseq-count -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf 2>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/8_dedup_counts/Group2_C2.deDup_counts.txt [Tue Nov 19 05:38:50 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=5000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:34:33 2024] rule rule_7_mark_dup: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C2.gene.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_C2.gene.MDunsorted.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_C2.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C2 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=5000, mem_mb_total=20000, runtime=02:30 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_C2_deDupMetrics /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C2.gene.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_C2.txt 2>&1 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MarkDuplicatesUMIbyGene.py --inputBam /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C2.gene.bam --outputBam /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_C2.gene.MDunsorted.bam --bcLength 8 --gtf /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf --outputMetricsDir /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_C2_deDupMetrics --outputPrefix dup_Group2_C2 --logFile /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_C2.txt >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_C2.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/7_mark_dup/Group2_C2.gene.MDunsorted.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/7_mark_dup.Group2_C2.txt 2>&1 [Tue Nov 19 05:36:01 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=5000, mem_mb_total=20000 Select jobs to execute... [Tue Nov 19 05:28:10 2024] rule rule_6_count_reads: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_C2.UMI.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C2.gene.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C2.gene.bam.bai log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group2_C2.samtools_view.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group2_C2.htseq_count.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C2 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=5000, mem_mb_total=20000, runtime=02:30 /opt/miniconda3/envs/utap/bin/samtools view -H /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_C2.UMI.out.bam -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C2.header.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group2_C2.samtools_view.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools view -h /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_C2.UMI.out.bam | /opt/miniconda3/envs/utap/bin/htseq-count -o /dev/fd/3 -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10-gencode.genes.3utr.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C2_counts.txt | /opt/miniconda3/envs/utap/bin/samtools view -Sb - > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C2.gene.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C2.gene.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/6_count_reads.Group2_C2.samtools_view.txt 2>&1 touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C2.gene.bam.deleted touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/6_count_reads/Group2_C2.gene.bam.bai.deleted 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 412669 GFF lines processed. 100000 alignment records processed. 200000 alignment records processed. 300000 alignment records processed. 400000 alignment records processed. 500000 alignment records processed. 600000 alignment records processed. 700000 alignment records processed. 800000 alignment records processed. 900000 alignment records processed. 1000000 alignment records processed. 1100000 alignment records processed. 1200000 alignment records processed. 1300000 alignment records processed. 1400000 alignment records processed. 1500000 alignment records processed. 1600000 alignment records processed. 1700000 alignment records processed. 1800000 alignment records processed. 1900000 alignment records processed. 2000000 alignment records processed. 2100000 alignment records processed. 2200000 alignment records processed. 2300000 alignment records processed. 2400000 alignment records processed. 2500000 alignment records processed. 2600000 alignment records processed. 2700000 alignment records processed. 2800000 alignment records processed. 2900000 alignment records processed. 3000000 alignment records processed. 3100000 alignment records processed. 3200000 alignment records processed. 3300000 alignment records processed. 3400000 alignment records processed. 3500000 alignment records processed. 3600000 alignment records processed. 3700000 alignment records processed. 3800000 alignment records processed. 3900000 alignment records processed. 4000000 alignment records processed. 4100000 alignment records processed. 4200000 alignment records processed. 4300000 alignment records processed. 4400000 alignment records processed. 4500000 alignment records processed. 4600000 alignment records processed. 4700000 alignment records processed. 4800000 alignment records processed. 4900000 alignment records processed. 5000000 alignment records processed. 5100000 alignment records processed. 5200000 alignment records processed. 5300000 alignment records processed. 5400000 alignment records processed. 5500000 alignment records processed. 5600000 alignment records processed. 5700000 alignment records processed. 5800000 alignment records processed. 5900000 alignment records processed. 6000000 alignment records processed. 6100000 alignment records processed. 6200000 alignment records processed. 6300000 alignment records processed. 6400000 alignment records processed. 6500000 alignment records processed. 6600000 alignment records processed. 6700000 alignment records processed. 6800000 alignment records processed. 6900000 alignment records processed. 7000000 alignment records processed. 7100000 alignment records processed. 7200000 alignment records processed. 7300000 alignment records processed. 7400000 alignment records processed. 7500000 alignment records processed. 7600000 alignment records processed. 7700000 alignment records processed. 7800000 alignment records processed. 7900000 alignment records processed. 8000000 alignment records processed. 8100000 alignment records processed. 8185131 alignment records processed. [Tue Nov 19 05:34:09 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=200, mem_mb_total=200 Select jobs to execute... [Tue Nov 19 05:26:38 2024] rule rule_5_move_umi: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C2Aligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_C2.UMI.out.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/5_move_umi.Group2_C2.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=200, mem_mb_total=200, runtime=02:30 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MoveBC.py --bamIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C2Aligned.sortedByCoord.out.bam --bamOut /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_C2.UMI.out.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/5_move_umi.Group2_C2.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/5_move_umi/Group2_C2.UMI.out.bam.deleted [Tue Nov 19 05:27:46 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Tue Nov 19 05:24:11 2024] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_C2/Group2_C2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C2Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C2Aligned.sortedByCoord.out.bam.bai log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/4_mapping.Group2_C2.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_C2 threads: 20 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --genomeDir /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/STAR_v2.7.10a_index/ --readFilesIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_C2/Group2_C2_R1.fastq.gz --readFilesCommand zcat --alignEndsType EndToEnd --runThreadN 20 --genomeLoad NoSharedMemory --outFilterMismatchNoverLmax 0.05 --outSAMstrandField intronMotif --twopassMode Basic --outSAMtype BAM SortedByCoordinate --alignSoftClipAtReferenceEnds No --outFileNamePrefix /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C2 --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/4_mapping.Group2_C2.txt 2>&1; /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C2Aligned.sortedByCoord.out.bam touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C2Aligned.sortedByCoord.out.bam.deleted touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/4_mapping/Group2_C2Aligned.sortedByCoord.out.bam.bai.deleted [Tue Nov 19 05:26:02 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Provided resources: mem_mb=1135, disk_mb=1135, mem_mb_per_thread=400, mem_mb_total=200 Select jobs to execute... [Tue Nov 19 04:46:24 2024] rule rule_1_combined_fastq: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group1_LPS2/Group1_LPS2_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group1_LPS2/Group1_LPS2_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_LPS2/Group1_LPS2.R1.combined.fastq.gz, /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_LPS2/Group1_LPS2.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/1_combined_fastq.Group1_LPS2.txt jobid: 0 reason: Forced execution wildcards: sample=Group1_LPS2 resources: mem_mb=1135, disk_mb=1135, tmpdir=/tmp, mem_mb_per_thread=400, mem_mb_total=200 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/ExtractBCSR.py --fastqIn /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group1_LPS2/Group1_LPS2_R1.fastq.gz --fastqUMI /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/fastq/Group1_LPS2/Group1_LPS2_R2.fastq.gz --fastqOut /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_LPS2/Group1_LPS2.R1.combined.fastq.gz --bcHistFileName /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_LPS2/Group1_LPS2.umi_frequencies.csv > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group1_LPS2/Group1_LPS2.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/1_combined_fastq.Group1_LPS2.txt [Tue Nov 19 04:58:40 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Tue Nov 19 04:58:57 2024] rule rule_3_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_LPS1/Group2_LPS1_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group2_LPS1/Group2_LPS1_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_fastqc.Group2_LPS1.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS1 threads: 5 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group2_LPS1 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/3_fastqc/Group2_LPS1 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_LPS1/Group2_LPS1_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/3_fastqc.Group2_LPS1.txt 2>&1 [Tue Nov 19 04:59:34 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['Group1_LPS1', 'Group1_C1', 'Group2_C2', 'Group1_LPS2', 'Group2_C1', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C2'] factors:['LPS', 'LPS', 'LPS', 'LPS', 'control', 'control', 'control', 'control'] deseq samples:['Group1_LPS1', 'Group1_LPS2', 'Group2_LPS1', 'Group2_LPS2', 'Group1_C1', 'Group1_C2', 'Group2_C1', 'Group2_C2'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Tue Nov 19 04:56:37 2024] rule rule_2_cutadapt: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_LPS1/Group2_LPS1.R1.combined.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_LPS1/Group2_LPS1_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/2_cutadapt.Group2_LPS1.txt jobid: 0 reason: Forced execution wildcards: sample=Group2_LPS1 threads: 4 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -j 4 --times 2 -u 1 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_LPS1/Group2_LPS1_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/1_combined_fastq/Group2_LPS1/Group2_LPS1.R1.combined.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_LPS1.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/logs_20241119_044604/2_cutadapt.Group2_LPS1.txt touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_MARS-seq_mm10/demo_LPS/20241119_044604_data_for_demo_production_Transcriptome_MARS-Seq/2_cutadapt/Group2_LPS1/Group2_LPS1_R1.fastq.gz.deleted [Tue Nov 19 04:57:03 2024] Finished job 0. 1 of 1 steps (100%) done