All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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=1009, disk_mb=1009, mem_mb_per_thread=400, mem_mb_total=200 Select jobs to execute... [Sun Feb 2 08:13:09 2025] rule rule_1_combined_fastq: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_base_R8/basal_base_R8_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_base_R8/basal_base_R8_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R8/basal_base_R8.R1.combined.fastq.gz, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R8/basal_base_R8.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/1_combined_fastq.basal_base_R8.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R8 resources: mem_mb=1009, disk_mb=1009, 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_SCRB_Keren_mm10/fastq/basal_base_R8/basal_base_R8_R1.fastq.gz --fastqUMI /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_base_R8/basal_base_R8_R2.fastq.gz --fastqOut /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R8/basal_base_R8.R1.combined.fastq.gz --bcHistFileName /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R8/basal_base_R8.umi_frequencies.csv > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R8/basal_base_R8.txt 2> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/1_combined_fastq.basal_base_R8.txt [Sun Feb 2 08:24:53 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:18:41 2025] rule rule_3_fastqc: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_M2/basal_tip_M2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_tip_M2/basal_tip_M2_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/3_fastqc.basal_tip_M2.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_M2 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_tip_M2 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_tip_M2 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_M2/basal_tip_M2_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/3_fastqc.basal_tip_M2.txt 2>&1 [Sun Feb 2 08:18:55 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:16:39 2025] rule rule_2_cutadapt: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_M2/basal_tip_M2.R1.combined.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_M2/basal_tip_M2_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/2_cutadapt.basal_tip_M2.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_M2 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_M2/basal_tip_M2_R1.fastq.gz /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_M2/basal_tip_M2.R1.combined.fastq.gz > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_M2.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/2_cutadapt.basal_tip_M2.txt touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_M2/basal_tip_M2_R1.fastq.gz.deleted [Sun Feb 2 08:16:50 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:13:09 2025] rule rule_1_combined_fastq: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_tip_M2/basal_tip_M2_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_tip_M2/basal_tip_M2_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_M2/basal_tip_M2.R1.combined.fastq.gz, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_M2/basal_tip_M2.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/1_combined_fastq.basal_tip_M2.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_M2 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_SCRB_Keren_mm10/fastq/basal_tip_M2/basal_tip_M2_R1.fastq.gz --fastqUMI /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_tip_M2/basal_tip_M2_R2.fastq.gz --fastqOut /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_M2/basal_tip_M2.R1.combined.fastq.gz --bcHistFileName /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_M2/basal_tip_M2.umi_frequencies.csv > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_M2/basal_tip_M2.txt 2> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/1_combined_fastq.basal_tip_M2.txt [Sun Feb 2 08:16:02 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:19:44 2025] rule rule_3_fastqc: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_R5/basal_tip_R5_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_tip_R5/basal_tip_R5_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/3_fastqc.basal_tip_R5.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R5 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_tip_R5 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_tip_R5 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_R5/basal_tip_R5_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/3_fastqc.basal_tip_R5.txt 2>&1 [Sun Feb 2 08:20:01 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:16:41 2025] rule rule_2_cutadapt: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_R5/basal_tip_R5.R1.combined.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_R5/basal_tip_R5_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/2_cutadapt.basal_tip_R5.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R5 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_R5/basal_tip_R5_R1.fastq.gz /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_R5/basal_tip_R5.R1.combined.fastq.gz > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_R5.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/2_cutadapt.basal_tip_R5.txt touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_R5/basal_tip_R5_R1.fastq.gz.deleted [Sun Feb 2 08:17:02 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:13:09 2025] rule rule_1_combined_fastq: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_tip_R5/basal_tip_R5_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_tip_R5/basal_tip_R5_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_R5/basal_tip_R5.R1.combined.fastq.gz, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_R5/basal_tip_R5.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/1_combined_fastq.basal_tip_R5.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R5 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_SCRB_Keren_mm10/fastq/basal_tip_R5/basal_tip_R5_R1.fastq.gz --fastqUMI /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_tip_R5/basal_tip_R5_R2.fastq.gz --fastqOut /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_R5/basal_tip_R5.R1.combined.fastq.gz --bcHistFileName /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_R5/basal_tip_R5.umi_frequencies.csv > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_R5/basal_tip_R5.txt 2> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/1_combined_fastq.basal_tip_R5.txt [Sun Feb 2 08:16:15 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:21:56 2025] rule rule_3_fastqc: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_R8/basal_tip_R8_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_tip_R8/basal_tip_R8_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/3_fastqc.basal_tip_R8.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R8 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_tip_R8 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_tip_R8 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_R8/basal_tip_R8_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/3_fastqc.basal_tip_R8.txt 2>&1 [Sun Feb 2 08:22:20 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:20:28 2025] rule rule_2_cutadapt: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_R8/basal_tip_R8.R1.combined.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_R8/basal_tip_R8_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/2_cutadapt.basal_tip_R8.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R8 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_R8/basal_tip_R8_R1.fastq.gz /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_R8/basal_tip_R8.R1.combined.fastq.gz > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_R8.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/2_cutadapt.basal_tip_R8.txt touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_R8/basal_tip_R8_R1.fastq.gz.deleted [Sun Feb 2 08:20:50 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:13:09 2025] rule rule_1_combined_fastq: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_tip_R8/basal_tip_R8_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_tip_R8/basal_tip_R8_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_R8/basal_tip_R8.R1.combined.fastq.gz, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_R8/basal_tip_R8.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/1_combined_fastq.basal_tip_R8.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R8 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_SCRB_Keren_mm10/fastq/basal_tip_R8/basal_tip_R8_R1.fastq.gz --fastqUMI /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_tip_R8/basal_tip_R8_R2.fastq.gz --fastqOut /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_R8/basal_tip_R8.R1.combined.fastq.gz --bcHistFileName /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_R8/basal_tip_R8.umi_frequencies.csv > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_tip_R8/basal_tip_R8.txt 2> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/1_combined_fastq.basal_tip_R8.txt [Sun Feb 2 08:20:07 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1881, disk_mb=1881, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Sun Feb 2 08:40:59 2025] rule rule_ngsplot: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/multiQC/multiqc_report.html, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_base_R3.deDup_counts.corrected.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_base_R5.deDup_counts.corrected.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_base_R8.deDup_counts.corrected.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_tip_M2.deDup_counts.corrected.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_tip_R5.deDup_counts.corrected.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_tip_R8.deDup_counts.corrected.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R3Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R5Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R8Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_M2Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R5Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R8Aligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/10_reports/ngsplotOut.avgprof.pdf log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/10_reports.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/ngsplot.txt jobid: 0 reason: Forced execution threads: 20 resources: mem_mb=1881, disk_mb=1881, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 [Sun Feb 2 08:44:46 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:26:59 2025] rule rule_3_multiQC: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_base_R3/basal_base_R3_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_base_R5/basal_base_R5_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_base_R8/basal_base_R8_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_tip_M2/basal_tip_M2_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_tip_R5/basal_tip_R5_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_tip_R8/basal_tip_R8_R1_fastqc/fastqc_data.txt output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/multiQC/multiqc_report.html log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/3_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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/multiQC /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc &>/home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/3_multiQC.txt [Sun Feb 2 08:27:03 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:24:08 2025] rule rule_9_umi_counts: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_base_R3.deDup_counts.txt output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_base_R3.deDup_counts.corrected.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/9_umi_counts.basal_base_R3.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R3 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_base_R3.deDup_counts.txt --bcLength 10 --outputCounts /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_base_R3.deDup_counts.corrected.txt > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/9_umi_counts.basal_base_R3.txt 2>&1 [Sun Feb 2 08:24:08 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:23:20 2025] rule rule_8_dedup_counts: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R3.gene.MDunsorted.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_base_R3.deDup_counts.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R3 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R3.gene.MDunsorted.bam | grep -v RX:Z:[ACTG]*N[ACTGN]* | cat /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R3.header.sam - | /opt/miniconda3/envs/utap/bin/htseq-count -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.3utr.gtf 2>&1 > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_base_R3.deDup_counts.txt [Sun Feb 2 08:23:48 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:22:42 2025] rule rule_7_mark_dup: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R3.gene.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R3.gene.MDunsorted.bam log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_base_R3.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R3 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R3_deDupMetrics /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R3.gene.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_base_R3.txt 2>&1 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MarkDuplicatesUMIbyGene.py --inputBam /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R3.gene.bam --outputBam /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R3.gene.MDunsorted.bam --bcLength 10 --gtf /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.3utr.gtf --outputMetricsDir /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R3_deDupMetrics --outputPrefix dup_basal_base_R3 --logFile /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_base_R3.txt >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_base_R3.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R3.gene.MDunsorted.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_base_R3.txt 2>&1 [Sun Feb 2 08:23:02 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:20:54 2025] rule rule_6_count_reads: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R3.UMI.out.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R3.gene.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R3.gene.bam.bai log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_base_R3.samtools_view.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_base_R3.htseq_count.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R3 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R3.UMI.out.bam -o /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R3.header.sam > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_base_R3.samtools_view.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools view -h /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R3.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.genes.3utr.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R3_counts.txt | /opt/miniconda3/envs/utap/bin/samtools view -Sb - > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R3.gene.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R3.gene.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_base_R3.samtools_view.txt 2>&1 touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R3.gene.bam.deleted touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R3.gene.bam.bai.deleted 100000 GFF lines processed. 109405 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. 2058171 alignment records processed. [Sun Feb 2 08:22:25 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:20:16 2025] rule rule_5_move_umi: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R3Aligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R3.UMI.out.bam log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/5_move_umi.basal_base_R3.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R3 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R3Aligned.sortedByCoord.out.bam --bamOut /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R3.UMI.out.bam > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/5_move_umi.basal_base_R3.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R3.UMI.out.bam.deleted [Sun Feb 2 08:20:33 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:16:44 2025] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R3/basal_base_R3_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R3Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R3Aligned.sortedByCoord.out.bam.bai log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/4_mapping.basal_base_R3.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R3 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R3/basal_base_R3_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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R3 --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/4_mapping.basal_base_R3.txt 2>&1; /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R3Aligned.sortedByCoord.out.bam touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R3Aligned.sortedByCoord.out.bam.deleted touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R3Aligned.sortedByCoord.out.bam.bai.deleted [Sun Feb 2 08:19:25 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:23:31 2025] rule rule_9_umi_counts: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_base_R5.deDup_counts.txt output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_base_R5.deDup_counts.corrected.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/9_umi_counts.basal_base_R5.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R5 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_base_R5.deDup_counts.txt --bcLength 10 --outputCounts /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_base_R5.deDup_counts.corrected.txt > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/9_umi_counts.basal_base_R5.txt 2>&1 [Sun Feb 2 08:23:32 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:23:00 2025] rule rule_8_dedup_counts: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R5.gene.MDunsorted.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_base_R5.deDup_counts.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R5 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R5.gene.MDunsorted.bam | grep -v RX:Z:[ACTG]*N[ACTGN]* | cat /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R5.header.sam - | /opt/miniconda3/envs/utap/bin/htseq-count -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.3utr.gtf 2>&1 > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_base_R5.deDup_counts.txt [Sun Feb 2 08:23:19 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:19:44 2025] rule rule_3_fastqc: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R3/basal_base_R3_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_base_R3/basal_base_R3_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/3_fastqc.basal_base_R3.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R3 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_base_R3 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_base_R3 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R3/basal_base_R3_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/3_fastqc.basal_base_R3.txt 2>&1 [Sun Feb 2 08:20:00 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:22:31 2025] rule rule_7_mark_dup: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R5.gene.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R5.gene.MDunsorted.bam log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_base_R5.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R5 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R5_deDupMetrics /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R5.gene.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_base_R5.txt 2>&1 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MarkDuplicatesUMIbyGene.py --inputBam /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R5.gene.bam --outputBam /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R5.gene.MDunsorted.bam --bcLength 10 --gtf /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.3utr.gtf --outputMetricsDir /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R5_deDupMetrics --outputPrefix dup_basal_base_R5 --logFile /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_base_R5.txt >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_base_R5.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R5.gene.MDunsorted.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_base_R5.txt 2>&1 [Sun Feb 2 08:22:40 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:20:43 2025] rule rule_6_count_reads: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R5.UMI.out.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R5.gene.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R5.gene.bam.bai log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_base_R5.samtools_view.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_base_R5.htseq_count.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R5 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R5.UMI.out.bam -o /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R5.header.sam > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_base_R5.samtools_view.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools view -h /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R5.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.genes.3utr.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R5_counts.txt | /opt/miniconda3/envs/utap/bin/samtools view -Sb - > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R5.gene.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R5.gene.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_base_R5.samtools_view.txt 2>&1 touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R5.gene.bam.deleted touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R5.gene.bam.bai.deleted 100000 GFF lines processed. 109405 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. 1287604 alignment records processed. [Sun Feb 2 08:21:35 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:20:17 2025] rule rule_5_move_umi: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R5Aligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R5.UMI.out.bam log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/5_move_umi.basal_base_R5.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R5 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R5Aligned.sortedByCoord.out.bam --bamOut /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R5.UMI.out.bam > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/5_move_umi.basal_base_R5.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R5.UMI.out.bam.deleted [Sun Feb 2 08:20:27 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:15:31 2025] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R5/basal_base_R5_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R5Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R5Aligned.sortedByCoord.out.bam.bai log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/4_mapping.basal_base_R5.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R5 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R5/basal_base_R5_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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R5 --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/4_mapping.basal_base_R5.txt 2>&1; /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R5Aligned.sortedByCoord.out.bam touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R5Aligned.sortedByCoord.out.bam.deleted touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R5Aligned.sortedByCoord.out.bam.bai.deleted [Sun Feb 2 08:18:29 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:39:57 2025] rule rule_9_umi_counts: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_base_R8.deDup_counts.txt output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_base_R8.deDup_counts.corrected.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/9_umi_counts.basal_base_R8.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R8 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_base_R8.deDup_counts.txt --bcLength 10 --outputCounts /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_base_R8.deDup_counts.corrected.txt > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/9_umi_counts.basal_base_R8.txt 2>&1 [Sun Feb 2 08:39:58 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:37:44 2025] rule rule_8_dedup_counts: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R8.gene.MDunsorted.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_base_R8.deDup_counts.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R8 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R8.gene.MDunsorted.bam | grep -v RX:Z:[ACTG]*N[ACTGN]* | cat /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R8.header.sam - | /opt/miniconda3/envs/utap/bin/htseq-count -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.3utr.gtf 2>&1 > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_base_R8.deDup_counts.txt [Sun Feb 2 08:39:42 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:36:41 2025] rule rule_7_mark_dup: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R8.gene.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R8.gene.MDunsorted.bam log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_base_R8.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R8 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R8_deDupMetrics /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R8.gene.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_base_R8.txt 2>&1 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MarkDuplicatesUMIbyGene.py --inputBam /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R8.gene.bam --outputBam /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R8.gene.MDunsorted.bam --bcLength 10 --gtf /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.3utr.gtf --outputMetricsDir /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R8_deDupMetrics --outputPrefix dup_basal_base_R8 --logFile /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_base_R8.txt >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_base_R8.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_base_R8.gene.MDunsorted.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_base_R8.txt 2>&1 [Sun Feb 2 08:37:27 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:31:20 2025] rule rule_6_count_reads: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R8.UMI.out.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R8.gene.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R8.gene.bam.bai log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_base_R8.samtools_view.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_base_R8.htseq_count.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R8 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R8.UMI.out.bam -o /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R8.header.sam > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_base_R8.samtools_view.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools view -h /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R8.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.genes.3utr.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R8_counts.txt | /opt/miniconda3/envs/utap/bin/samtools view -Sb - > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R8.gene.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R8.gene.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_base_R8.samtools_view.txt 2>&1 touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R8.gene.bam.deleted touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_base_R8.gene.bam.bai.deleted 100000 GFF lines processed. 109405 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. 8507560 alignment records processed. [Sun Feb 2 08:36:27 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:30:03 2025] rule rule_5_move_umi: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R8Aligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R8.UMI.out.bam log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/5_move_umi.basal_base_R8.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R8 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R8Aligned.sortedByCoord.out.bam --bamOut /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R8.UMI.out.bam > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/5_move_umi.basal_base_R8.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_base_R8.UMI.out.bam.deleted [Sun Feb 2 08:31:02 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:26:06 2025] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R8/basal_base_R8_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R8Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R8Aligned.sortedByCoord.out.bam.bai log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/4_mapping.basal_base_R8.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R8 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R8/basal_base_R8_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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R8 --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/4_mapping.basal_base_R8.txt 2>&1; /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R8Aligned.sortedByCoord.out.bam touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R8Aligned.sortedByCoord.out.bam.deleted touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_base_R8Aligned.sortedByCoord.out.bam.bai.deleted [Sun Feb 2 08:29:47 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:16:21 2025] rule rule_2_cutadapt: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R3/basal_base_R3.R1.combined.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R3/basal_base_R3_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/2_cutadapt.basal_base_R3.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R3 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R3/basal_base_R3_R1.fastq.gz /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R3/basal_base_R3.R1.combined.fastq.gz > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R3.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/2_cutadapt.basal_base_R3.txt touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R3/basal_base_R3_R1.fastq.gz.deleted [Sun Feb 2 08:16:30 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:24:38 2025] rule rule_9_umi_counts: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_tip_M2.deDup_counts.txt output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_tip_M2.deDup_counts.corrected.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/9_umi_counts.basal_tip_M2.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_M2 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_tip_M2.deDup_counts.txt --bcLength 10 --outputCounts /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_tip_M2.deDup_counts.corrected.txt > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/9_umi_counts.basal_tip_M2.txt 2>&1 [Sun Feb 2 08:24:38 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:23:31 2025] rule rule_8_dedup_counts: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_M2.gene.MDunsorted.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_tip_M2.deDup_counts.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_M2 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_M2.gene.MDunsorted.bam | grep -v RX:Z:[ACTG]*N[ACTGN]* | cat /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_M2.header.sam - | /opt/miniconda3/envs/utap/bin/htseq-count -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.3utr.gtf 2>&1 > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_tip_M2.deDup_counts.txt [Sun Feb 2 08:24:13 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:23:01 2025] rule rule_7_mark_dup: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_M2.gene.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_M2.gene.MDunsorted.bam log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_tip_M2.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_M2 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_M2_deDupMetrics /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_M2.gene.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_tip_M2.txt 2>&1 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MarkDuplicatesUMIbyGene.py --inputBam /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_M2.gene.bam --outputBam /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_M2.gene.MDunsorted.bam --bcLength 10 --gtf /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.3utr.gtf --outputMetricsDir /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_M2_deDupMetrics --outputPrefix dup_basal_tip_M2 --logFile /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_tip_M2.txt >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_tip_M2.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_M2.gene.MDunsorted.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_tip_M2.txt 2>&1 [Sun Feb 2 08:23:18 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:20:29 2025] rule rule_6_count_reads: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_M2.UMI.out.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_M2.gene.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_M2.gene.bam.bai log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_tip_M2.samtools_view.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_tip_M2.htseq_count.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_M2 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_M2.UMI.out.bam -o /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_M2.header.sam > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_tip_M2.samtools_view.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools view -h /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_M2.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.genes.3utr.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_M2_counts.txt | /opt/miniconda3/envs/utap/bin/samtools view -Sb - > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_M2.gene.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_M2.gene.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_tip_M2.samtools_view.txt 2>&1 touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_M2.gene.bam.deleted touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_M2.gene.bam.bai.deleted 100000 GFF lines processed. 109405 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. 2763464 alignment records processed. [Sun Feb 2 08:22:33 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:19:51 2025] rule rule_5_move_umi: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_M2Aligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_M2.UMI.out.bam log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/5_move_umi.basal_tip_M2.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_M2 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_M2Aligned.sortedByCoord.out.bam --bamOut /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_M2.UMI.out.bam > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/5_move_umi.basal_tip_M2.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_M2.UMI.out.bam.deleted [Sun Feb 2 08:20:11 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:17:04 2025] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_M2/basal_tip_M2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_M2Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_M2Aligned.sortedByCoord.out.bam.bai log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/4_mapping.basal_tip_M2.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_M2 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_M2/basal_tip_M2_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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_M2 --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/4_mapping.basal_tip_M2.txt 2>&1; /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_M2Aligned.sortedByCoord.out.bam touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_M2Aligned.sortedByCoord.out.bam.deleted touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_M2Aligned.sortedByCoord.out.bam.bai.deleted [Sun Feb 2 08:19:15 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:23:31 2025] rule rule_9_umi_counts: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_tip_R5.deDup_counts.txt output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_tip_R5.deDup_counts.corrected.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/9_umi_counts.basal_tip_R5.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R5 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_tip_R5.deDup_counts.txt --bcLength 10 --outputCounts /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_tip_R5.deDup_counts.corrected.txt > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/9_umi_counts.basal_tip_R5.txt 2>&1 [Sun Feb 2 08:23:32 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:22:42 2025] rule rule_8_dedup_counts: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_R5.gene.MDunsorted.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_tip_R5.deDup_counts.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R5 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_R5.gene.MDunsorted.bam | grep -v RX:Z:[ACTG]*N[ACTGN]* | cat /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R5.header.sam - | /opt/miniconda3/envs/utap/bin/htseq-count -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.3utr.gtf 2>&1 > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_tip_R5.deDup_counts.txt [Sun Feb 2 08:23:13 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:22:19 2025] rule rule_7_mark_dup: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R5.gene.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_R5.gene.MDunsorted.bam log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_tip_R5.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R5 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_R5_deDupMetrics /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R5.gene.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_tip_R5.txt 2>&1 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MarkDuplicatesUMIbyGene.py --inputBam /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R5.gene.bam --outputBam /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_R5.gene.MDunsorted.bam --bcLength 10 --gtf /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.3utr.gtf --outputMetricsDir /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_R5_deDupMetrics --outputPrefix dup_basal_tip_R5 --logFile /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_tip_R5.txt >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_tip_R5.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_R5.gene.MDunsorted.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_tip_R5.txt 2>&1 [Sun Feb 2 08:22:32 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:20:20 2025] rule rule_6_count_reads: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_R5.UMI.out.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R5.gene.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R5.gene.bam.bai log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_tip_R5.samtools_view.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_tip_R5.htseq_count.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R5 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_R5.UMI.out.bam -o /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R5.header.sam > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_tip_R5.samtools_view.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools view -h /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_R5.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.genes.3utr.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R5_counts.txt | /opt/miniconda3/envs/utap/bin/samtools view -Sb - > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R5.gene.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R5.gene.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_tip_R5.samtools_view.txt 2>&1 touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R5.gene.bam.deleted touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R5.gene.bam.bai.deleted 100000 GFF lines processed. 109405 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. 2328746 alignment records processed. [Sun Feb 2 08:21:58 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:13:09 2025] rule rule_1_combined_fastq: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_base_R3/basal_base_R3_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_base_R3/basal_base_R3_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R3/basal_base_R3.R1.combined.fastq.gz, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R3/basal_base_R3.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/1_combined_fastq.basal_base_R3.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R3 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_SCRB_Keren_mm10/fastq/basal_base_R3/basal_base_R3_R1.fastq.gz --fastqUMI /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_base_R3/basal_base_R3_R2.fastq.gz --fastqOut /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R3/basal_base_R3.R1.combined.fastq.gz --bcHistFileName /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R3/basal_base_R3.umi_frequencies.csv > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R3/basal_base_R3.txt 2> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/1_combined_fastq.basal_base_R3.txt [Sun Feb 2 08:16:06 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:19:51 2025] rule rule_5_move_umi: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R5Aligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_R5.UMI.out.bam log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/5_move_umi.basal_tip_R5.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R5 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R5Aligned.sortedByCoord.out.bam --bamOut /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_R5.UMI.out.bam > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/5_move_umi.basal_tip_R5.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_R5.UMI.out.bam.deleted [Sun Feb 2 08:20:08 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:17:16 2025] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_R5/basal_tip_R5_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R5Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R5Aligned.sortedByCoord.out.bam.bai log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/4_mapping.basal_tip_R5.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R5 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_R5/basal_tip_R5_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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R5 --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/4_mapping.basal_tip_R5.txt 2>&1; /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R5Aligned.sortedByCoord.out.bam touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R5Aligned.sortedByCoord.out.bam.deleted touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R5Aligned.sortedByCoord.out.bam.bai.deleted [Sun Feb 2 08:19:12 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:31:27 2025] rule rule_9_umi_counts: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_tip_R8.deDup_counts.txt output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_tip_R8.deDup_counts.corrected.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/9_umi_counts.basal_tip_R8.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R8 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_tip_R8.deDup_counts.txt --bcLength 10 --outputCounts /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/9_umi_counts/basal_tip_R8.deDup_counts.corrected.txt > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/9_umi_counts.basal_tip_R8.txt 2>&1 [Sun Feb 2 08:31:28 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:30:12 2025] rule rule_8_dedup_counts: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_R8.gene.MDunsorted.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_tip_R8.deDup_counts.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R8 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_R8.gene.MDunsorted.bam | grep -v RX:Z:[ACTG]*N[ACTGN]* | cat /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R8.header.sam - | /opt/miniconda3/envs/utap/bin/htseq-count -i gene_name - /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.3utr.gtf 2>&1 > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/8_dedup_counts/basal_tip_R8.deDup_counts.txt [Sun Feb 2 08:31:18 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:27:49 2025] rule rule_7_mark_dup: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R8.gene.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_R8.gene.MDunsorted.bam log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_tip_R8.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R8 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_R8_deDupMetrics /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R8.gene.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_tip_R8.txt 2>&1 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/MarkDuplicatesUMIbyGene.py --inputBam /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R8.gene.bam --outputBam /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_R8.gene.MDunsorted.bam --bcLength 10 --gtf /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.3utr.gtf --outputMetricsDir /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_R8_deDupMetrics --outputPrefix dup_basal_tip_R8 --logFile /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_tip_R8.txt >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_tip_R8.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/7_mark_dup/basal_tip_R8.gene.MDunsorted.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/7_mark_dup.basal_tip_R8.txt 2>&1 [Sun Feb 2 08:30:00 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:24:09 2025] rule rule_6_count_reads: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_R8.UMI.out.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R8.gene.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R8.gene.bam.bai log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_tip_R8.samtools_view.txt, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_tip_R8.htseq_count.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R8 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_R8.UMI.out.bam -o /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R8.header.sam > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_tip_R8.samtools_view.txt 2>&1 /opt/miniconda3/envs/utap/bin/samtools view -h /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_R8.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.genes.3utr.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R8_counts.txt | /opt/miniconda3/envs/utap/bin/samtools view -Sb - > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R8.gene.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R8.gene.bam >> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/6_count_reads.basal_tip_R8.samtools_view.txt 2>&1 touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R8.gene.bam.deleted touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/6_count_reads/basal_tip_R8.gene.bam.bai.deleted 100000 GFF lines processed. 109405 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. 5639885 alignment records processed. [Sun Feb 2 08:27:29 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:23:06 2025] rule rule_5_move_umi: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R8Aligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_R8.UMI.out.bam log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/5_move_umi.basal_tip_R8.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R8 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R8Aligned.sortedByCoord.out.bam --bamOut /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_R8.UMI.out.bam > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/5_move_umi.basal_tip_R8.txt 2>&1; touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/5_move_umi/basal_tip_R8.UMI.out.bam.deleted [Sun Feb 2 08:23:46 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:21:07 2025] rule rule_4_mapping: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_R8/basal_tip_R8_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R8Aligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R8Aligned.sortedByCoord.out.bam.bai log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/4_mapping.basal_tip_R8.txt jobid: 0 reason: Forced execution wildcards: sample=basal_tip_R8 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_tip_R8/basal_tip_R8_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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R8 --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/4_mapping.basal_tip_R8.txt 2>&1; /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R8Aligned.sortedByCoord.out.bam touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R8Aligned.sortedByCoord.out.bam.deleted touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/4_mapping/basal_tip_R8Aligned.sortedByCoord.out.bam.bai.deleted [Sun Feb 2 08:23:02 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:16:09 2025] rule rule_3_fastqc: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R5/basal_base_R5_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_base_R5/basal_base_R5_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/3_fastqc.basal_base_R5.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R5 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_base_R5 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_base_R5 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R5/basal_base_R5_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/3_fastqc.basal_base_R5.txt 2>&1 [Sun Feb 2 08:16:18 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:15:09 2025] rule rule_2_cutadapt: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R5/basal_base_R5.R1.combined.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R5/basal_base_R5_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/2_cutadapt.basal_base_R5.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R5 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R5/basal_base_R5_R1.fastq.gz /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R5/basal_base_R5.R1.combined.fastq.gz > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R5.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/2_cutadapt.basal_base_R5.txt touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R5/basal_base_R5_R1.fastq.gz.deleted [Sun Feb 2 08:15:16 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:13:09 2025] rule rule_1_combined_fastq: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_base_R5/basal_base_R5_R1.fastq.gz, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_base_R5/basal_base_R5_R2.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R5/basal_base_R5.R1.combined.fastq.gz, /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R5/basal_base_R5.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/1_combined_fastq.basal_base_R5.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R5 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_SCRB_Keren_mm10/fastq/basal_base_R5/basal_base_R5_R1.fastq.gz --fastqUMI /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/fastq/basal_base_R5/basal_base_R5_R2.fastq.gz --fastqOut /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R5/basal_base_R5.R1.combined.fastq.gz --bcHistFileName /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R5/basal_base_R5.umi_frequencies.csv > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R5/basal_base_R5.txt 2> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/1_combined_fastq.basal_base_R5.txt [Sun Feb 2 08:14:53 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:26:06 2025] rule rule_3_fastqc: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R8/basal_base_R8_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_base_R8/basal_base_R8_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/3_fastqc.basal_base_R8.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R8 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_base_R8 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/3_fastqc/basal_base_R8 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R8/basal_base_R8_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/3_fastqc.basal_base_R8.txt 2>&1 [Sun Feb 2 08:26:43 2025] Finished job 0. 1 of 1 steps (100%) done All samples:['basal_base_R8', 'basal_tip_R8', 'basal_tip_M2', 'basal_base_R5', 'basal_tip_R5', 'basal_base_R3'] factors:['basal_base', 'basal_base', 'basal_base', 'basal_tip', 'basal_tip', 'basal_tip'] deseq samples:['basal_base_R3', 'basal_base_R5', 'basal_base_R8', 'basal_tip_M2', 'basal_tip_R5', 'basal_tip_R8'] 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... [Sun Feb 2 08:25:12 2025] rule rule_2_cutadapt: input: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R8/basal_base_R8.R1.combined.fastq.gz output: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R8/basal_base_R8_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/2_cutadapt.basal_base_R8.txt jobid: 0 reason: Forced execution wildcards: sample=basal_base_R8 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_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R8/basal_base_R8_R1.fastq.gz /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/1_combined_fastq/basal_base_R8/basal_base_R8.R1.combined.fastq.gz > /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R8.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/logs_20250202_101250/2_cutadapt.basal_base_R8.txt touch /home/labs/bioservices/Collaboration/example_SCRB_Keren_mm10/20250202_101250_Keren_short_Transcriptome_SCRB-Seq/2_cutadapt/basal_base_R8/basal_base_R8_R1.fastq.gz.deleted [Sun Feb 2 08:25:49 2025] Finished job 0. 1 of 1 steps (100%) done