['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=5970, disk_mb=5970, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Mon Nov 18 23:06:22 2024] rule rule_4_cutadapt_filter_length: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RKD1_no_rRNA_cutadapt.fastq output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD1_no_rRNA_25_32.fastq log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/4_cutadapt_filter_length.RKD1.txt jobid: 0 reason: Forced execution wildcards: sample=RKD1 threads: 4 resources: mem_mb=5970, disk_mb=5970, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -m 25 -M 32 -j 4 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD1_no_rRNA_25_32.fastq /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RKD1_no_rRNA_cutadapt.fastq > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD1.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/4_cutadapt_filter_length.RKD1.txt [Mon Nov 18 23:06:35 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1524, disk_mb=1524, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 23:02:58 2024] rule rule_3_bowtie_rRNA: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RKD1/RKD1_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RKD1_no_rRNA_cutadapt.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RKD1_rRNA.sam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/3_bowtie_rRNA_RKD1.txt jobid: 0 reason: Forced execution wildcards: sample=RKD1 threads: 20 resources: mem_mb=1524, disk_mb=1524, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/bowtie -p 20 -norc --un /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RKD1_no_rRNA_cutadapt.fastq /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/bowtie1_rRNA_index/rRNA /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RKD1/RKD1_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RKD1_rRNA.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RKD1_bowtie_summary.txt 2>&1 [Mon Nov 18 23:03:40 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=2372, disk_mb=2372, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Mon Nov 18 22:53:51 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/fastq/RKD1/RKD1_S3_L007_R1_001.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RKD1/RKD1_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/1_cutadapt.RKD1.txt jobid: 0 reason: Forced execution wildcards: sample=RKD1 threads: 4 resources: mem_mb=2372, disk_mb=2372, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --discard-untrimmed -j 4 --times 1 -u 1 -m 20 -M 50 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RKD1/RKD1_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/fastq/RKD1/RKD1_S3_L007_R1_001.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RKD1.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/1_cutadapt.RKD1.txt [Mon Nov 18 22:56:28 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=5166, disk_mb=5166, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Mon Nov 18 23:06:06 2024] rule rule_4_cutadapt_filter_length: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RKD2_no_rRNA_cutadapt.fastq output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD2_no_rRNA_25_32.fastq log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/4_cutadapt_filter_length.RKD2.txt jobid: 0 reason: Forced execution wildcards: sample=RKD2 threads: 4 resources: mem_mb=5166, disk_mb=5166, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -m 25 -M 32 -j 4 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD2_no_rRNA_25_32.fastq /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RKD2_no_rRNA_cutadapt.fastq > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD2.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/4_cutadapt_filter_length.RKD2.txt [Mon Nov 18 23:07:10 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1385, disk_mb=1385, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 23:04:20 2024] rule rule_3_bowtie_rRNA: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RKD2/RKD2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RKD2_no_rRNA_cutadapt.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RKD2_rRNA.sam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/3_bowtie_rRNA_RKD2.txt jobid: 0 reason: Forced execution wildcards: sample=RKD2 threads: 20 resources: mem_mb=1385, disk_mb=1385, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/bowtie -p 20 -norc --un /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RKD2_no_rRNA_cutadapt.fastq /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/bowtie1_rRNA_index/rRNA /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RKD2/RKD2_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RKD2_rRNA.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RKD2_bowtie_summary.txt 2>&1 [Mon Nov 18 23:05:10 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=3059, disk_mb=3059, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Mon Nov 18 22:53:51 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/fastq/RKD2/RKD2_S4_L007_R1_001.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RKD2/RKD2_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/1_cutadapt.RKD2.txt jobid: 0 reason: Forced execution wildcards: sample=RKD2 threads: 4 resources: mem_mb=3059, disk_mb=3059, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --discard-untrimmed -j 4 --times 1 -u 1 -m 20 -M 50 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RKD2/RKD2_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/fastq/RKD2/RKD2_S4_L007_R1_001.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RKD2.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/1_cutadapt.RKD2.txt [Mon Nov 18 22:56:37 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=15925, disk_mb=15925, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Mon Nov 18 23:33:19 2024] rule rule_5_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC1_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC2_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD1_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD2_no_rRNA_25_32.fastq output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RNC2_25_32/RNC2_no_rRNA_25_32_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/5_fastqc_RNC2_25_32.txt jobid: 0 reason: Forced execution wildcards: sample=RNC2 threads: 5 resources: mem_mb=15925, disk_mb=15925, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RNC2_25_32 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RNC2_25_32 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC1_no_rRNA_25_32.fastq /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC2_no_rRNA_25_32.fastq /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD1_no_rRNA_25_32.fastq /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD2_no_rRNA_25_32.fastq > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/5_fastqc_RNC2_25_32.txt 2>&1 [Mon Nov 18 23:33:53 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=15925, disk_mb=15925, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Mon Nov 18 23:33:08 2024] rule rule_5_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC1_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC2_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD1_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD2_no_rRNA_25_32.fastq output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RKD1_25_32/RKD1_no_rRNA_25_32_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/5_fastqc_RKD1_25_32.txt jobid: 0 reason: Forced execution wildcards: sample=RKD1 threads: 5 resources: mem_mb=15925, disk_mb=15925, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RKD1_25_32 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RKD1_25_32 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC1_no_rRNA_25_32.fastq /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC2_no_rRNA_25_32.fastq /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD1_no_rRNA_25_32.fastq /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD2_no_rRNA_25_32.fastq > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/5_fastqc_RKD1_25_32.txt 2>&1 [Mon Nov 18 23:33:50 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=15925, disk_mb=15925, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Mon Nov 18 23:32:10 2024] rule rule_5_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC1_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC2_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD1_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD2_no_rRNA_25_32.fastq output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RKD2_25_32/RKD2_no_rRNA_25_32_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/5_fastqc_RKD2_25_32.txt jobid: 0 reason: Forced execution wildcards: sample=RKD2 threads: 5 resources: mem_mb=15925, disk_mb=15925, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RKD2_25_32 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RKD2_25_32 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC1_no_rRNA_25_32.fastq /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC2_no_rRNA_25_32.fastq /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD1_no_rRNA_25_32.fastq /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD2_no_rRNA_25_32.fastq > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/5_fastqc_RKD2_25_32.txt 2>&1 [Mon Nov 18 23:32:53 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:32:31 2024] rule rule_9_tdf: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC1_tophat.filtered.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/9_tdf/RNC1_tophat.filtered.tdf log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/9_tdf.RNC1.txt jobid: 0 reason: Forced execution wildcards: sample=RNC1 threads: 20 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 cd /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/9_tdf; /opt/miniconda3/envs/utap/bin/igvtools count -z 5 -w 1 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC1_tophat.filtered.bam /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/9_tdf/RNC1_tophat.filtered.tdf /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes INFO [Nov 18,2024 21:32] [Globals] Development mode is enabled INFO [Nov 18,2024 21:32] [GenomeManager] Loading genome: /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes WARNING: BAM index file /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC1_tophat.filtered.bam.bai is older than BAM /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC1_tophat.filtered.bam WARNING: BAM index file /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC1_tophat.filtered.bam.bai is older than BAM /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC1_tophat.filtered.bam INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr1 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr10 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr11 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr12 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr13 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr14 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr15 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr16 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr17 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr18 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr19 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr1_GL456221_random INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr2 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr3 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr4 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr4_GL456216_random INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr4_JH584295_random INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr5 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr6 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr7 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr8 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr9 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chrM INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chrUn_GL456239 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chrUn_JH584304 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chrX INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chrX_GL456233_random INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chrY [Mon Nov 18 23:32:55 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 10 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1000, disk_mb=1000, mem_mb_per_thread=3000, mem_mb_total=30000 Select jobs to execute... [Mon Nov 18 23:43:16 2024] rule rule_14_reports: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/6_multiQC/multiqc_report.html, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/9_tdf/RNC1_tophat.filtered.tdf, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/9_tdf/RNC2_tophat.filtered.tdf, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/9_tdf/RKD1_tophat.filtered.tdf, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/9_tdf/RKD2_tophat.filtered.tdf, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/11_merge_htseq_counts/merged.htseq.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/multiQC/multiqc_report.html, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks/RNC1_summits.bed, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks/RNC2_summits.bed, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks/RKD1_summits.bed, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks/RKD2_summits.bed, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/13_shif_and_extend_summit/RNC1_sh13_ex3.bed, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/13_shif_and_extend_summit/RNC2_sh13_ex3.bed, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/13_shif_and_extend_summit/RKD1_sh13_ex3.bed, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/13_shif_and_extend_summit/RKD2_sh13_ex3.bed, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RNC1/RNC1_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RNC2/RNC2_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RKD1/RKD1_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RKD2/RKD2_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RNC1_25_32/RNC1_no_rRNA_25_32_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RNC2_25_32/RNC2_no_rRNA_25_32_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RKD1_25_32/RKD1_no_rRNA_25_32_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RKD2_25_32/RKD2_no_rRNA_25_32_fastqc/fastqc_data.txt output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/Done_20241118_225323.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/14_reports.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/counts_log.txt jobid: 0 reason: Forced execution threads: 10 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=30000 PATH=$PATH:/opt/miniconda3/envs/utap/bin export HOME=$HOME mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/run-fastqc-report-table.py --fastqc-dir /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc --output-file-base /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/fastqc_Per_base_sequence_quality /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/run-fastqc-report-table.py --fastqc-dir /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc --output-file-base /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/fastqc_Per_base_sequence_quality_2 /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/PrepareFilesToReport.py --pipeline-dir /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq --output-dir /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports --samples RNC1 RNC2 RKD1 RKD2 --run-id 20241118_225323 --paired no --samples-treatment None --samples-control None --logFile /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/14_reports.txt; /opt/miniconda3/envs/utap/bin/python /opt/miniconda3/envs/utap/bin/ReportsCounts.py --pipeline-dir /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq --output /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/counts_all_steps.txt --samples RNC1 RNC2 RKD1 RKD2 --stranded "no" --paired no --logFile /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/counts_log.txt cp /opt/miniconda3/envs/utap/lib/python3.10/site-packages/ngs-snakemake/report_functions.R /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323 cp /opt/miniconda3/envs/utap/lib/python3.10/site-packages/ngs-snakemake/report_Chromatin_pipelines.Rmd /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323 cp /opt/miniconda3/envs/utap/lib/python3.10/site-packages/ngs-snakemake/Sequencing_and_Mapping_QC_extend.Rmd /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323 cp /opt/miniconda3/envs/utap/lib/python3.10/site-packages/ngs-snakemake/header.html /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323 cp /opt/miniconda3/envs/utap/lib/python3.10/site-packages/ngs-snakemake/wis_logo_heb_v1.png /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323 sed -i 's/JOB_NAME/20241118_225323_data_for_demo_production/g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/RUN_ID/20241118_225323/g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/COMMANDS_LOG/commands_log_20241118_225323.txt/g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/R_LIB_PATHS/"\/opt\/miniconda3\/envs\/utap\/lib\/R\/library"/g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_functions.R sed -i 's/PIPELINE_TYPE/Ribo-Seq/g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/SUBTITLE//g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/GENOME/mm10/g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/GENOME/mm10/g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/Sequencing_and_Mapping_QC_extend.Rmd sed -i 's/CUTADAPT_CUT_START//g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/CUTADAPT_CUT_END//g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/CUTADAPT_QVALUE/20/g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/CUTADAPT_MIN_LEN/25/g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/CUTADAPT_MAX_LEN/32/g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/CUTADAPT_MIN_LEN/25/g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/Sequencing_and_Mapping_QC_extend.Rmd sed -i 's/ADAPTOR1/CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/ADAPTOR2//g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's@INPUT_FOLDER@/home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/fastq@g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's@OUTPUT_FOLDER@/home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq@g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/FASTQC/2_fastqc/g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's@REPORT_OUTPUT_DIR@data_for_demo_production_20241118_225323@g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/COMMANDS_LOG/commands_log_20241118_225323.txt/g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's@YAML_PATH@/home/labs/bioservices/services/UTAP-data/utap-meta-data/installation/UTAP-data-singularity/utap_update/reports/20241118_225323_data_for_demo_production_analysis_parameters.yaml@g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's@PAIRED@no@g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's@UTAP_VERSION@2.0@g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's@ngsplot_eval <- TRUE@ngsplot_eval <- FALSE@g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's@TREAT_VS_CONTROL@None@g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/ADDITIONAL_ADAPTER_R1//g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/ADDITIONAL_ADAPTER_R2//g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's/CUTADAPT_TIMES/1/g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's@BLACK_LIST@None@g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's@MACS2_BANDWIDTH@300@g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's@MACS2_QVALUE@0.05@g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's@SHIFT@13@g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd sed -i 's@EXTEND@3@g' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd \/opt\/miniconda3\/envs\/utap\/bin\/Rscript -e "rmarkdown::render('/home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/14_reports/data_for_demo_production_20241118_225323/report_Chromatin_pipelines.Rmd')" --verbose >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/14_reports.txt 2>&1 touch /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/Done_20241118_225323.txt [Mon Nov 18 23:44:25 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:32:11 2024] rule rule_8_samtools_filter: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RNC1_tophat.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC1_tophat.filtered.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/8_samtools_filter.RNC1.txt jobid: 0 reason: Forced execution wildcards: sample=RNC1 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/samtools view -b -q 10 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RNC1_tophat.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC1_tophat.filtered.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC1_tophat.filtered.bam [Mon Nov 18 23:32:22 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=15925, disk_mb=15925, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 23:10:59 2024] rule rule_7_tophat: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC1_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC2_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD1_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD2_no_rRNA_25_32.fastq output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RNC1_tophat.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/7_tophat.RNC1.txt jobid: 0 reason: Forced execution wildcards: sample=RNC1 threads: 20 resources: mem_mb=15925, disk_mb=15925, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/ngsplot/bin/tophat -N 1 --no-novel-juncs --library-type fr-firststrand -p 20 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RNC1 --GTF /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.gtf /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/mm10 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC1_no_rRNA_25_32.fastq > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/7_tophat.RNC1.txt 2>&1 mv /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RNC1/accepted_hits.bam /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RNC1_tophat.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RNC1_tophat.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/7_tophat.RNC1.txt 2>&1 [Mon Nov 18 23:31:53 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:40:37 2024] rule rule_9_tdf: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC2_tophat.filtered.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/9_tdf/RNC2_tophat.filtered.tdf log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/9_tdf.RNC2.txt jobid: 0 reason: Forced execution wildcards: sample=RNC2 threads: 20 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 cd /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/9_tdf; /opt/miniconda3/envs/utap/bin/igvtools count -z 5 -w 1 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC2_tophat.filtered.bam /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/9_tdf/RNC2_tophat.filtered.tdf /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes INFO [Nov 18,2024 21:40] [Globals] Development mode is enabled INFO [Nov 18,2024 21:40] [GenomeManager] Loading genome: /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes WARNING: BAM index file /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC2_tophat.filtered.bam.bai is older than BAM /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC2_tophat.filtered.bam WARNING: BAM index file /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC2_tophat.filtered.bam.bai is older than BAM /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC2_tophat.filtered.bam INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr1 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr10 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr11 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr12 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr13 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr14 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr15 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr16 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr17 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr18 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr19 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr2 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr3 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr4 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr4_GL456216_random INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr4_JH584295_random INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr5 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr6 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr7 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr8 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chr9 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chrM INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chrUn_GL456239 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chrUn_JH584304 INFO [Nov 18,2024 21:40] [Preprocessor] Processing chromosome chrX INFO [Nov 18,2024 21:41] [Preprocessor] Processing chromosome chrX_GL456233_random INFO [Nov 18,2024 21:41] [Preprocessor] Processing chromosome chrY [Mon Nov 18 23:41:26 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1303, disk_mb=1303, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 23:39:33 2024] rule rule_8_samtools_filter: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RNC2_tophat.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC2_tophat.filtered.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/8_samtools_filter.RNC2.txt jobid: 0 reason: Forced execution wildcards: sample=RNC2 threads: 20 resources: mem_mb=1303, disk_mb=1303, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/samtools view -b -q 10 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RNC2_tophat.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC2_tophat.filtered.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC2_tophat.filtered.bam [Mon Nov 18 23:39:46 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=15925, disk_mb=15925, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 23:10:55 2024] rule rule_7_tophat: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC1_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC2_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD1_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD2_no_rRNA_25_32.fastq output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RNC2_tophat.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/7_tophat.RNC2.txt jobid: 0 reason: Forced execution wildcards: sample=RNC2 threads: 20 resources: mem_mb=15925, disk_mb=15925, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/ngsplot/bin/tophat -N 1 --no-novel-juncs --library-type fr-firststrand -p 20 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RNC2 --GTF /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.gtf /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/mm10 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC2_no_rRNA_25_32.fastq > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/7_tophat.RNC2.txt 2>&1 mv /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RNC2/accepted_hits.bam /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RNC2_tophat.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RNC2_tophat.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/7_tophat.RNC2.txt 2>&1 [Mon Nov 18 23:35:53 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:32:44 2024] rule rule_9_tdf: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD1_tophat.filtered.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/9_tdf/RKD1_tophat.filtered.tdf log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/9_tdf.RKD1.txt jobid: 0 reason: Forced execution wildcards: sample=RKD1 threads: 20 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 cd /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/9_tdf; /opt/miniconda3/envs/utap/bin/igvtools count -z 5 -w 1 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD1_tophat.filtered.bam /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/9_tdf/RKD1_tophat.filtered.tdf /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes INFO [Nov 18,2024 21:32] [Globals] Development mode is enabled INFO [Nov 18,2024 21:32] [GenomeManager] Loading genome: /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes WARNING: BAM index file /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD1_tophat.filtered.bam.bai is older than BAM /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD1_tophat.filtered.bam WARNING: BAM index file /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD1_tophat.filtered.bam.bai is older than BAM /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD1_tophat.filtered.bam INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr1 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr10 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr11 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr12 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr13 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr14 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr15 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr16 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr17 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr18 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr19 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr2 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr3 INFO [Nov 18,2024 21:32] [Preprocessor] Processing chromosome chr4 INFO [Nov 18,2024 21:33] [Preprocessor] Processing chromosome chr4_GL456216_random INFO [Nov 18,2024 21:33] [Preprocessor] Processing chromosome chr4_JH584295_random INFO [Nov 18,2024 21:33] [Preprocessor] Processing chromosome chr5 INFO [Nov 18,2024 21:33] [Preprocessor] Processing chromosome chr6 INFO [Nov 18,2024 21:33] [Preprocessor] Processing chromosome chr7 INFO [Nov 18,2024 21:33] [Preprocessor] Processing chromosome chr8 INFO [Nov 18,2024 21:33] [Preprocessor] Processing chromosome chr9 INFO [Nov 18,2024 21:33] [Preprocessor] Processing chromosome chrM INFO [Nov 18,2024 21:33] [Preprocessor] Processing chromosome chrUn_GL456239 INFO [Nov 18,2024 21:33] [Preprocessor] Processing chromosome chrUn_JH584304 INFO [Nov 18,2024 21:33] [Preprocessor] Processing chromosome chrX INFO [Nov 18,2024 21:33] [Preprocessor] Processing chromosome chrX_GL456233_random INFO [Nov 18,2024 21:33] [Preprocessor] Processing chromosome chrY [Mon Nov 18 23:33:05 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:32:21 2024] rule rule_8_samtools_filter: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RKD1_tophat.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD1_tophat.filtered.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/8_samtools_filter.RKD1.txt jobid: 0 reason: Forced execution wildcards: sample=RKD1 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/samtools view -b -q 10 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RKD1_tophat.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD1_tophat.filtered.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD1_tophat.filtered.bam [Mon Nov 18 23:32:31 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=15925, disk_mb=15925, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 23:11:43 2024] rule rule_7_tophat: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC1_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC2_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD1_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD2_no_rRNA_25_32.fastq output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RKD1_tophat.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/7_tophat.RKD1.txt jobid: 0 reason: Forced execution wildcards: sample=RKD1 threads: 20 resources: mem_mb=15925, disk_mb=15925, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/ngsplot/bin/tophat -N 1 --no-novel-juncs --library-type fr-firststrand -p 20 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RKD1 --GTF /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.gtf /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/mm10 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD1_no_rRNA_25_32.fastq > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/7_tophat.RKD1.txt 2>&1 mv /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RKD1/accepted_hits.bam /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RKD1_tophat.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RKD1_tophat.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/7_tophat.RKD1.txt 2>&1 [Mon Nov 18 23:32:08 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:30:05 2024] rule rule_9_tdf: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD2_tophat.filtered.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/9_tdf/RKD2_tophat.filtered.tdf log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/9_tdf.RKD2.txt jobid: 0 reason: Forced execution wildcards: sample=RKD2 threads: 20 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 cd /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/9_tdf; /opt/miniconda3/envs/utap/bin/igvtools count -z 5 -w 1 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD2_tophat.filtered.bam /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/9_tdf/RKD2_tophat.filtered.tdf /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes INFO [Nov 18,2024 21:30] [Globals] Development mode is enabled INFO [Nov 18,2024 21:30] [GenomeManager] Loading genome: /shareDB/genomes/Mus_musculus/UCSC/mm10/Chrom_sizes/mm10.chrom.sizes WARNING: BAM index file /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD2_tophat.filtered.bam.bai is older than BAM /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD2_tophat.filtered.bam WARNING: BAM index file /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD2_tophat.filtered.bam.bai is older than BAM /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD2_tophat.filtered.bam INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr1 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr10 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr11 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr12 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr13 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr14 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr15 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr16 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr17 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr18 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr19 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr2 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr3 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr4 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr4_GL456216_random INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr4_JH584295_random INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr5 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr6 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr7 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr8 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chr9 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chrM INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chrUn_GL456239 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chrUn_JH584304 INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chrX INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chrX_GL456233_random INFO [Nov 18,2024 21:30] [Preprocessor] Processing chromosome chrY [Mon Nov 18 23:30:29 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:27:46 2024] rule rule_8_samtools_filter: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RKD2_tophat.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD2_tophat.filtered.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/8_samtools_filter.RKD2.txt jobid: 0 reason: Forced execution wildcards: sample=RKD2 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/samtools view -b -q 10 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RKD2_tophat.bam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD2_tophat.filtered.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD2_tophat.filtered.bam [Mon Nov 18 23:27:54 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:35:07 2024] rule rule_6_multiQC: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RNC1_25_32/RNC1_no_rRNA_25_32_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RNC2_25_32/RNC2_no_rRNA_25_32_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RKD1_25_32/RKD1_no_rRNA_25_32_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RKD2_25_32/RKD2_no_rRNA_25_32_fastqc/fastqc_data.txt output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/6_multiQC/multiqc_report.html log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/6_multiQC.txt jobid: 0 reason: Forced execution resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=1000, mem_mb_total=1000 /opt/miniconda3/envs/utap/bin/multiqc -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/6_multiQC /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc &>/home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/6_multiQC.txt [Mon Nov 18 23:35:14 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=15925, disk_mb=15925, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 23:08:40 2024] rule rule_7_tophat: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC1_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC2_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD1_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD2_no_rRNA_25_32.fastq output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RKD2_tophat.bam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/7_tophat.RKD2.txt jobid: 0 reason: Forced execution wildcards: sample=RKD2 threads: 20 resources: mem_mb=15925, disk_mb=15925, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/ngsplot/bin/tophat -N 1 --no-novel-juncs --library-type fr-firststrand -p 20 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RKD2 --GTF /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.gtf /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/mm10 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD2_no_rRNA_25_32.fastq > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/7_tophat.RKD2.txt 2>&1 mv /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RKD2/accepted_hits.bam /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RKD2_tophat.bam /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/7_tophat/RKD2_tophat.bam >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/7_tophat.RKD2.txt 2>&1 [Mon Nov 18 23:27:29 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:42:22 2024] rule rule_11_merge_htseq_counts: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/10_count_reads/RNC1_counts.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/10_count_reads/RNC2_counts.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/10_count_reads/RKD1_counts.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/10_count_reads/RKD2_counts.txt output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/11_merge_htseq_counts/merged.htseq.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/11_merge_htseq_counts.RNC1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/11_merge_htseq_counts.RNC2.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/11_merge_htseq_counts.RKD1.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/11_merge_htseq_counts.RKD2.txt jobid: 0 reason: Forced execution resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=300, mem_mb_total=300 awk 'NF > 1{ a[$1] = a[$1]" "$2} END {for( i in a ) print i a[i]}' /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/10_count_reads/RNC1_counts.txt /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/10_count_reads/RNC2_counts.txt /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/10_count_reads/RKD1_counts.txt /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/10_count_reads/RKD2_counts.txt >> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/11_merge_htseq_counts/merged.htseq.txt [Mon Nov 18 23:42:23 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:36:09 2024] rule rule_10_htseq_count: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC1_tophat.filtered.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/10_count_reads/RNC1_counts.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/10_htseq_count.RNC1.txt jobid: 0 reason: Forced execution wildcards: sample=RNC1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=300, mem_mb_total=300 /opt/miniconda3/envs/utap/bin/htseq-count /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC1_tophat.filtered.bam -f bam -s yes -t exon -m intersection-nonempty -i gene_id /shareDB/genomes/Mus_musculus/UCSC/mm10/Annotation/HTSeq_Annotation_cds_UTR_without_overlap/mm10_cds_UTR_without_overlap.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/10_count_reads/RNC1_counts.txt [W::hts_idx_load3] The index file is older than the data file: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC1_tophat.filtered.bam.bai 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 500000 GFF lines processed. 600000 GFF lines processed. 700000 GFF lines processed. 779598 GFF lines processed. [W::hts_idx_load3] The index file is older than the data file: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC1_tophat.filtered.bam.bai 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. 3513170 alignment records processed. [Mon Nov 18 23:37:43 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:40:05 2024] rule rule_10_htseq_count: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC2_tophat.filtered.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/10_count_reads/RNC2_counts.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/10_htseq_count.RNC2.txt jobid: 0 reason: Forced execution wildcards: sample=RNC2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=300, mem_mb_total=300 /opt/miniconda3/envs/utap/bin/htseq-count /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC2_tophat.filtered.bam -f bam -s yes -t exon -m intersection-nonempty -i gene_id /shareDB/genomes/Mus_musculus/UCSC/mm10/Annotation/HTSeq_Annotation_cds_UTR_without_overlap/mm10_cds_UTR_without_overlap.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/10_count_reads/RNC2_counts.txt [W::hts_idx_load3] The index file is older than the data file: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC2_tophat.filtered.bam.bai 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 500000 GFF lines processed. 600000 GFF lines processed. 700000 GFF lines processed. 779598 GFF lines processed. [W::hts_idx_load3] The index file is older than the data file: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC2_tophat.filtered.bam.bai 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. 3300693 alignment records processed. [Mon Nov 18 23:41:54 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:34:05 2024] rule rule_10_htseq_count: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD1_tophat.filtered.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/10_count_reads/RKD1_counts.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/10_htseq_count.RKD1.txt jobid: 0 reason: Forced execution wildcards: sample=RKD1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=300, mem_mb_total=300 /opt/miniconda3/envs/utap/bin/htseq-count /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD1_tophat.filtered.bam -f bam -s yes -t exon -m intersection-nonempty -i gene_id /shareDB/genomes/Mus_musculus/UCSC/mm10/Annotation/HTSeq_Annotation_cds_UTR_without_overlap/mm10_cds_UTR_without_overlap.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/10_count_reads/RKD1_counts.txt [W::hts_idx_load3] The index file is older than the data file: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD1_tophat.filtered.bam.bai 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 500000 GFF lines processed. 600000 GFF lines processed. 700000 GFF lines processed. 779598 GFF lines processed. [W::hts_idx_load3] The index file is older than the data file: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD1_tophat.filtered.bam.bai 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. 3924299 alignment records processed. [Mon Nov 18 23:35:59 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:33:19 2024] rule rule_10_htseq_count: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD2_tophat.filtered.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/10_count_reads/RKD2_counts.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/10_htseq_count.RKD2.txt jobid: 0 reason: Forced execution wildcards: sample=RKD2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=300, mem_mb_total=300 /opt/miniconda3/envs/utap/bin/htseq-count /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD2_tophat.filtered.bam -f bam -s yes -t exon -m intersection-nonempty -i gene_id /shareDB/genomes/Mus_musculus/UCSC/mm10/Annotation/HTSeq_Annotation_cds_UTR_without_overlap/mm10_cds_UTR_without_overlap.gtf 3>&1 > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/10_count_reads/RKD2_counts.txt [W::hts_idx_load3] The index file is older than the data file: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD2_tophat.filtered.bam.bai 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 500000 GFF lines processed. 600000 GFF lines processed. 700000 GFF lines processed. 779598 GFF lines processed. [W::hts_idx_load3] The index file is older than the data file: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD2_tophat.filtered.bam.bai 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. 3433104 alignment records processed. [Mon Nov 18 23:34:52 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:07:08 2024] rule rule_2_multiQC: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RNC1/RNC1_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RNC2/RNC2_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RKD1/RKD1_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RKD2/RKD2_R1_fastqc/fastqc_data.txt output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/multiQC/multiqc_report.html log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/2_multiQC.txt jobid: 0 reason: Forced execution resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=1000, mem_mb_total=1000 /opt/miniconda3/envs/utap/bin/multiqc -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/multiQC /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc &>/home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/2_multiQC.txt [Mon Nov 18 23:07:13 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1429, disk_mb=1429, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Mon Nov 18 23:05:25 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RNC1/RNC1_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RNC1/RNC1_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/2_fastqc.RNC1.txt jobid: 0 reason: Forced execution wildcards: sample=RNC1 threads: 5 resources: mem_mb=1429, disk_mb=1429, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RNC1 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RNC1 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RNC1/RNC1_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/2_fastqc.RNC1.txt 2>&1 [Mon Nov 18 23:06:45 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1531, disk_mb=1531, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Mon Nov 18 23:04:38 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RNC2/RNC2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RNC2/RNC2_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/2_fastqc.RNC2.txt jobid: 0 reason: Forced execution wildcards: sample=RNC2 threads: 5 resources: mem_mb=1531, disk_mb=1531, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RNC2 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RNC2 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RNC2/RNC2_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/2_fastqc.RNC2.txt 2>&1 [Mon Nov 18 23:06:03 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1524, disk_mb=1524, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Mon Nov 18 23:05:24 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RKD1/RKD1_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RKD1/RKD1_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/2_fastqc.RKD1.txt jobid: 0 reason: Forced execution wildcards: sample=RKD1 threads: 5 resources: mem_mb=1524, disk_mb=1524, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RKD1 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RKD1 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RKD1/RKD1_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/2_fastqc.RKD1.txt 2>&1 [Mon Nov 18 23:06:51 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=15925, disk_mb=15925, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Mon Nov 18 23:30:49 2024] rule rule_5_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC1_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC2_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD1_no_rRNA_25_32.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD2_no_rRNA_25_32.fastq output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RNC1_25_32/RNC1_no_rRNA_25_32_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/5_fastqc_RNC1_25_32.txt jobid: 0 reason: Forced execution wildcards: sample=RNC1 threads: 5 resources: mem_mb=15925, disk_mb=15925, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RNC1_25_32 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/5_fastqc/RNC1_25_32 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC1_no_rRNA_25_32.fastq /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC2_no_rRNA_25_32.fastq /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD1_no_rRNA_25_32.fastq /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RKD2_no_rRNA_25_32.fastq > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/5_fastqc_RNC1_25_32.txt 2>&1 [Mon Nov 18 23:31:45 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1385, disk_mb=1385, mem_mb_per_thread=6000, mem_mb_total=30000 Select jobs to execute... [Mon Nov 18 23:03:52 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RKD2/RKD2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RKD2/RKD2_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/2_fastqc.RKD2.txt jobid: 0 reason: Forced execution wildcards: sample=RKD2 threads: 5 resources: mem_mb=1385, disk_mb=1385, tmpdir=/tmp, mem_mb_per_thread=6000, mem_mb_total=30000 mkdir -p /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RKD2 /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/2_fastqc/RKD2 -f fastq --threads 5 /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RKD2/RKD2_R1.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/2_fastqc.RKD2.txt 2>&1 [Mon Nov 18 23:05:07 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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=3000, mem_mb_total=3000 Select jobs to execute... [Mon Nov 18 23:35:39 2024] rule rule_12_macs_peaks: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC1_tophat.filtered.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks/RNC1_summits.bed log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/12_macs_peaks_RNC1.txt jobid: 0 reason: Forced execution wildcards: sample=RNC1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=3000 cd /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks; /opt/miniconda3/envs/utap/bin/macs2 callpeak -t /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC1_tophat.filtered.bam -f BAM -g mm --keep-dup all -n RNC1 --nomodel --extsize=1 --outdir /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks &>/home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/12_macs_peaks_RNC1.txt [Mon Nov 18 23:35:50 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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=3000, mem_mb_total=3000 Select jobs to execute... [Mon Nov 18 23:40:05 2024] rule rule_12_macs_peaks: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC2_tophat.filtered.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks/RNC2_summits.bed log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/12_macs_peaks_RNC2.txt jobid: 0 reason: Forced execution wildcards: sample=RNC2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=3000 cd /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks; /opt/miniconda3/envs/utap/bin/macs2 callpeak -t /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RNC2_tophat.filtered.bam -f BAM -g mm --keep-dup all -n RNC2 --nomodel --extsize=1 --outdir /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks &>/home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/12_macs_peaks_RNC2.txt [Mon Nov 18 23:40:15 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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=3000, mem_mb_total=3000 Select jobs to execute... [Mon Nov 18 23:35:06 2024] rule rule_12_macs_peaks: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD1_tophat.filtered.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks/RKD1_summits.bed log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/12_macs_peaks_RKD1.txt jobid: 0 reason: Forced execution wildcards: sample=RKD1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=3000 cd /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks; /opt/miniconda3/envs/utap/bin/macs2 callpeak -t /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD1_tophat.filtered.bam -f BAM -g mm --keep-dup all -n RKD1 --nomodel --extsize=1 --outdir /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks &>/home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/12_macs_peaks_RKD1.txt [Mon Nov 18 23:35:14 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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=3000, mem_mb_total=3000 Select jobs to execute... [Mon Nov 18 23:34:05 2024] rule rule_12_macs_peaks: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD2_tophat.filtered.bam output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks/RKD2_summits.bed log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/12_macs_peaks_RKD2.txt jobid: 0 reason: Forced execution wildcards: sample=RKD2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=3000 cd /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks; /opt/miniconda3/envs/utap/bin/macs2 callpeak -t /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/8_samtools_filter/RKD2_tophat.filtered.bam -f BAM -g mm --keep-dup all -n RKD2 --nomodel --extsize=1 --outdir /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks &>/home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/12_macs_peaks_RKD2.txt [Mon Nov 18 23:34:12 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:36:11 2024] rule rule_13_shif_and_extend_summit: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks/RNC1_summits.bed output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/13_shif_and_extend_summit/RNC1_sh13_ex3.bed log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/13_shif_and_extend_summit.RNC1_sh13_ex3.txt jobid: 0 reason: Forced execution wildcards: sample=RNC1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=1000, mem_mb_total=1000, runtime=02:30 /opt/miniconda3/envs/utap/bin/bedtools sort -i /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks/RNC1_summits.bed | intersectBed -wao -a - -b /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.gtf | cut -f1-5,12 | uniq | awk 'BEGIN {OFS=" "} { if($6 == "-") print $1, $2 - (13 + 3), $3 - (13 - 3), $4, $5, $6, $7; else if ($6 == "+") print $1, $2 + (13 - 3), $3 + (13 + 3), $4, $5, $6, $7; }' > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/13_shif_and_extend_summit/RNC1_sh13_ex3.bed [Mon Nov 18 23:36:14 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:40:39 2024] rule rule_13_shif_and_extend_summit: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks/RNC2_summits.bed output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/13_shif_and_extend_summit/RNC2_sh13_ex3.bed log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/13_shif_and_extend_summit.RNC2_sh13_ex3.txt jobid: 0 reason: Forced execution wildcards: sample=RNC2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=1000, mem_mb_total=1000, runtime=02:30 /opt/miniconda3/envs/utap/bin/bedtools sort -i /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks/RNC2_summits.bed | intersectBed -wao -a - -b /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.gtf | cut -f1-5,12 | uniq | awk 'BEGIN {OFS=" "} { if($6 == "-") print $1, $2 - (13 + 3), $3 - (13 - 3), $4, $5, $6, $7; else if ($6 == "+") print $1, $2 + (13 - 3), $3 + (13 + 3), $4, $5, $6, $7; }' > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/13_shif_and_extend_summit/RNC2_sh13_ex3.bed [Mon Nov 18 23:40:43 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:35:40 2024] rule rule_13_shif_and_extend_summit: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks/RKD1_summits.bed output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/13_shif_and_extend_summit/RKD1_sh13_ex3.bed log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/13_shif_and_extend_summit.RKD1_sh13_ex3.txt jobid: 0 reason: Forced execution wildcards: sample=RKD1 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=1000, mem_mb_total=1000, runtime=02:30 /opt/miniconda3/envs/utap/bin/bedtools sort -i /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks/RKD1_summits.bed | intersectBed -wao -a - -b /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.gtf | cut -f1-5,12 | uniq | awk 'BEGIN {OFS=" "} { if($6 == "-") print $1, $2 - (13 + 3), $3 - (13 - 3), $4, $5, $6, $7; else if ($6 == "+") print $1, $2 + (13 - 3), $3 + (13 + 3), $4, $5, $6, $7; }' > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/13_shif_and_extend_summit/RKD1_sh13_ex3.bed [Mon Nov 18 23:35:42 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None 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... [Mon Nov 18 23:34:37 2024] rule rule_13_shif_and_extend_summit: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks/RKD2_summits.bed output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/13_shif_and_extend_summit/RKD2_sh13_ex3.bed log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/13_shif_and_extend_summit.RKD2_sh13_ex3.txt jobid: 0 reason: Forced execution wildcards: sample=RKD2 resources: mem_mb=1000, disk_mb=1000, tmpdir=/tmp, mem_mb_per_thread=1000, mem_mb_total=1000, runtime=02:30 /opt/miniconda3/envs/utap/bin/bedtools sort -i /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/12_macs_peaks/RKD2_summits.bed | intersectBed -wao -a - -b /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.gtf | cut -f1-5,12 | uniq | awk 'BEGIN {OFS=" "} { if($6 == "-") print $1, $2 - (13 + 3), $3 - (13 - 3), $4, $5, $6, $7; else if ($6 == "+") print $1, $2 + (13 - 3), $3 + (13 + 3), $4, $5, $6, $7; }' > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/13_shif_and_extend_summit/RKD2_sh13_ex3.bed [Mon Nov 18 23:34:39 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=5095, disk_mb=5095, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Mon Nov 18 23:06:58 2024] rule rule_4_cutadapt_filter_length: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RNC1_no_rRNA_cutadapt.fastq output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC1_no_rRNA_25_32.fastq log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/4_cutadapt_filter_length.RNC1.txt jobid: 0 reason: Forced execution wildcards: sample=RNC1 threads: 4 resources: mem_mb=5095, disk_mb=5095, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -m 25 -M 32 -j 4 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC1_no_rRNA_25_32.fastq /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RNC1_no_rRNA_cutadapt.fastq > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC1.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/4_cutadapt_filter_length.RNC1.txt [Mon Nov 18 23:08:03 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1429, disk_mb=1429, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 23:03:44 2024] rule rule_3_bowtie_rRNA: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RNC1/RNC1_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RNC1_no_rRNA_cutadapt.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RNC1_rRNA.sam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/3_bowtie_rRNA_RNC1.txt jobid: 0 reason: Forced execution wildcards: sample=RNC1 threads: 20 resources: mem_mb=1429, disk_mb=1429, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/bowtie -p 20 -norc --un /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RNC1_no_rRNA_cutadapt.fastq /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/bowtie1_rRNA_index/rRNA /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RNC1/RNC1_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RNC1_rRNA.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RNC1_bowtie_summary.txt 2>&1 [Mon Nov 18 23:04:21 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=3167, disk_mb=3167, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Mon Nov 18 22:53:51 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/fastq/RNC1/RNC1_S1_L007_R1_001.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RNC1/RNC1_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/1_cutadapt.RNC1.txt jobid: 0 reason: Forced execution wildcards: sample=RNC1 threads: 4 resources: mem_mb=3167, disk_mb=3167, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --discard-untrimmed -j 4 --times 1 -u 1 -m 20 -M 50 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RNC1/RNC1_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/fastq/RNC1/RNC1_S1_L007_R1_001.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RNC1.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/1_cutadapt.RNC1.txt [Mon Nov 18 22:56:38 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=5822, disk_mb=5822, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Mon Nov 18 23:05:24 2024] rule rule_4_cutadapt_filter_length: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RNC2_no_rRNA_cutadapt.fastq output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC2_no_rRNA_25_32.fastq log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/4_cutadapt_filter_length.RNC2.txt jobid: 0 reason: Forced execution wildcards: sample=RNC2 threads: 4 resources: mem_mb=5822, disk_mb=5822, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -m 25 -M 32 -j 4 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC2_no_rRNA_25_32.fastq /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RNC2_no_rRNA_cutadapt.fastq > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/4_cutadapt_filter_length/RNC2.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/4_cutadapt_filter_length.RNC2.txt [Mon Nov 18 23:05:36 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1531, disk_mb=1531, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 23:04:26 2024] rule rule_3_bowtie_rRNA: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RNC2/RNC2_R1.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RNC2_no_rRNA_cutadapt.fastq, /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RNC2_rRNA.sam log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/3_bowtie_rRNA_RNC2.txt jobid: 0 reason: Forced execution wildcards: sample=RNC2 threads: 20 resources: mem_mb=1531, disk_mb=1531, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/bowtie -p 20 -norc --un /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RNC2_no_rRNA_cutadapt.fastq /shareDB/genomes/Mus_musculus/UCSC/mm10/Sequence/bowtie1_rRNA_index/rRNA /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RNC2/RNC2_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RNC2_rRNA.sam > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/3_bowtie_rRNA/RNC2_bowtie_summary.txt 2>&1 [Mon Nov 18 23:05:09 2024] Finished job 0. 1 of 1 steps (100%) done ['RNC1', 'RNC2', 'RKD1', 'RKD2'] {} None None Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=3644, disk_mb=3644, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Mon Nov 18 22:53:51 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/fastq/RNC2/RNC2_S2_L007_R1_001.fastq.gz output: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RNC2/RNC2_R1.fastq.gz log: /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/1_cutadapt.RNC2.txt jobid: 0 reason: Forced execution wildcards: sample=RNC2 threads: 4 resources: mem_mb=3644, disk_mb=3644, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --discard-untrimmed -j 4 --times 1 -u 1 -m 20 -M 50 -o /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RNC2/RNC2_R1.fastq.gz /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/fastq/RNC2/RNC2_S2_L007_R1_001.fastq.gz > /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/1_cutadapt/RNC2.cutadapt.txt 2> /home/labs/bioservices/Collaboration/example_and_data_for_testing_ribo-seq_mm10/20241118_225323_data_for_demo_production_Ribo-Seq/logs_20241118_225323/1_cutadapt.RNC2.txt [Mon Nov 18 22:57:01 2024] Finished job 0. 1 of 1 steps (100%) done