All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1510, disk_mb=1510, 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/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IQ-siYAP/IQ-siYAP_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siYAP/IQ-siYAP_R1.fastq.gz log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IQ-siYAP.txt jobid: 0 reason: Forced execution wildcards: sample=IQ-siYAP threads: 4 resources: mem_mb=1510, disk_mb=1510, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -a "T{10}" -j 4 --times 2 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siYAP/IQ-siYAP_R1.fastq.gz /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IQ-siYAP/IQ-siYAP_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siYAP.cutadapt.txt 2> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IQ-siYAP.txt && touch /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siYAP/IQ-siYAP_R1.fastq.gz.deleted [Mon Nov 18 22:55:11 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=5853, disk_mb=5853, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Mon Nov 18 23:04:30 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siYAP/IY-siYAP_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IY-siYAP/IY-siYAP_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IY-siYAP.txt jobid: 0 reason: Forced execution wildcards: sample=IY-siYAP threads: 5 resources: mem_mb=5853, disk_mb=5853, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IY-siYAP /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IY-siYAP -f fastq --threads 5 /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siYAP/IY-siYAP_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IY-siYAP.txt 2>&1 [Mon Nov 18 23:09:09 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=6303, disk_mb=6303, 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/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IY-siYAP/IY-siYAP_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siYAP/IY-siYAP_R1.fastq.gz log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IY-siYAP.txt jobid: 0 reason: Forced execution wildcards: sample=IY-siYAP threads: 4 resources: mem_mb=6303, disk_mb=6303, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -a "T{10}" -j 4 --times 2 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siYAP/IY-siYAP_R1.fastq.gz /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IY-siYAP/IY-siYAP_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siYAP.cutadapt.txt 2> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IY-siYAP.txt && touch /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siYAP/IY-siYAP_R1.fastq.gz.deleted [Mon Nov 18 22:58:10 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=2355, disk_mb=2355, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Mon Nov 18 23:04:27 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siYAP/IZ-siYAP_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IZ-siYAP/IZ-siYAP_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IZ-siYAP.txt jobid: 0 reason: Forced execution wildcards: sample=IZ-siYAP threads: 5 resources: mem_mb=2355, disk_mb=2355, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IZ-siYAP /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IZ-siYAP -f fastq --threads 5 /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siYAP/IZ-siYAP_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IZ-siYAP.txt 2>&1 [Mon Nov 18 23:06:19 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=2544, disk_mb=2544, 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/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IZ-siYAP/IZ-siYAP_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siYAP/IZ-siYAP_R1.fastq.gz log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IZ-siYAP.txt jobid: 0 reason: Forced execution wildcards: sample=IZ-siYAP threads: 4 resources: mem_mb=2544, disk_mb=2544, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -a "T{10}" -j 4 --times 2 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siYAP/IZ-siYAP_R1.fastq.gz /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IZ-siYAP/IZ-siYAP_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siYAP.cutadapt.txt 2> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IZ-siYAP.txt && touch /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siYAP/IZ-siYAP_R1.fastq.gz.deleted [Mon Nov 18 22:55:53 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1991, disk_mb=1991, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Mon Nov 18 23:03:07 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siC/IQ-siC_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IQ-siC/IQ-siC_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IQ-siC.txt jobid: 0 reason: Forced execution wildcards: sample=IQ-siC threads: 5 resources: mem_mb=1991, disk_mb=1991, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IQ-siC /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IQ-siC -f fastq --threads 5 /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siC/IQ-siC_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IQ-siC.txt 2>&1 [Mon Nov 18 23:04:42 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=2140, disk_mb=2140, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Mon Nov 18 22:53:52 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IQ-siC/IQ-siC_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siC/IQ-siC_R1.fastq.gz log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IQ-siC.txt jobid: 0 reason: Forced execution wildcards: sample=IQ-siC threads: 4 resources: mem_mb=2140, disk_mb=2140, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -a "T{10}" -j 4 --times 2 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siC/IQ-siC_R1.fastq.gz /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IQ-siC/IQ-siC_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siC.cutadapt.txt 2> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IQ-siC.txt && touch /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siC/IQ-siC_R1.fastq.gz.deleted [Mon Nov 18 22:55:36 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=5283, disk_mb=5283, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Mon Nov 18 23:02:55 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siC/IY-siC_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IY-siC/IY-siC_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IY-siC.txt jobid: 0 reason: Forced execution wildcards: sample=IY-siC threads: 5 resources: mem_mb=5283, disk_mb=5283, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IY-siC /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IY-siC -f fastq --threads 5 /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siC/IY-siC_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IY-siC.txt 2>&1 [Mon Nov 18 23:07:00 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=5717, disk_mb=5717, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Mon Nov 18 22:53:53 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IY-siC/IY-siC_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siC/IY-siC_R1.fastq.gz log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IY-siC.txt jobid: 0 reason: Forced execution wildcards: sample=IY-siC threads: 4 resources: mem_mb=5717, disk_mb=5717, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -a "T{10}" -j 4 --times 2 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siC/IY-siC_R1.fastq.gz /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IY-siC/IY-siC_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siC.cutadapt.txt 2> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IY-siC.txt && touch /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siC/IY-siC_R1.fastq.gz.deleted [Mon Nov 18 22:58:01 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1709, disk_mb=1709, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Mon Nov 18 23:02:55 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siC/IZ-siC_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IZ-siC/IZ-siC_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IZ-siC.txt jobid: 0 reason: Forced execution wildcards: sample=IZ-siC threads: 5 resources: mem_mb=1709, disk_mb=1709, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IZ-siC /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IZ-siC -f fastq --threads 5 /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siC/IZ-siC_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IZ-siC.txt 2>&1 [Mon Nov 18 23:04:10 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1835, disk_mb=1835, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Mon Nov 18 22:53:54 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IZ-siC/IZ-siC_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siC/IZ-siC_R1.fastq.gz log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IZ-siC.txt jobid: 0 reason: Forced execution wildcards: sample=IZ-siC threads: 4 resources: mem_mb=1835, disk_mb=1835, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -a "T{10}" -j 4 --times 2 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siC/IZ-siC_R1.fastq.gz /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IZ-siC/IZ-siC_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siC.cutadapt.txt 2> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IZ-siC.txt && touch /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siC/IZ-siC_R1.fastq.gz.deleted [Mon Nov 18 22:55:26 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=23007, disk_mb=23007, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 23:16:18 2024] rule rule_ngsplot: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IQ-siTAZAligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IY-siTAZAligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IZ-siTAZAligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IQ-siYAPAligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IY-siYAPAligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IZ-siYAPAligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IQ-siCAligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IY-siCAligned.sortedByCoord.out.bam, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IZ-siCAligned.sortedByCoord.out.bam output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/4_reports/ngsplotOut.avgprof.pdf log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/4_reports.txt, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/ngsplot.txt jobid: 0 reason: Forced execution threads: 20 resources: mem_mb=23007, disk_mb=23007, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 [Mon Nov 18 23:32:03 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=2690, disk_mb=2690, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 22:59:19 2024] rule rule_3_mapping: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siTAZ/IQ-siTAZ_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IQ-siTAZAligned.sortedByCoord.out.bam log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IQ-siTAZ.txt jobid: 0 reason: Forced execution wildcards: sample=IQ-siTAZ threads: 20 resources: mem_mb=2690, disk_mb=2690, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --alignEndsType EndToEnd --outFilterMismatchNoverLmax 0.05 --genomeDir /shareDB/genomes/Homo_sapiens/UCSC/hg38/Sequence/hg38_star_v2.7.10a_index --readFilesIn /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siTAZ/IQ-siTAZ_R1.fastq.gz --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --twopassMode Basic --runThreadN 20 --sjdbGTFfile /home/labs/bioservices/services/ngs/support/gtf/hg38-gencode.genes.gtf --quantMode GeneCounts --readFilesCommand zcat --outFileNamePrefix /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IQ-siTAZ --genomeLoad NoSharedMemory --sjdbGTFtagExonParentGene gene_name --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IQ-siTAZ.txt 2>&1 export HOME=$HOME /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IQ-siTAZAligned.sortedByCoord.out.bam >> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IQ-siTAZ.txt 2>&1 [Mon Nov 18 23:05:23 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=3099, disk_mb=3099, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 23:02:41 2024] rule rule_3_mapping: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siTAZ/IY-siTAZ_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IY-siTAZAligned.sortedByCoord.out.bam log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IY-siTAZ.txt jobid: 0 reason: Forced execution wildcards: sample=IY-siTAZ threads: 20 resources: mem_mb=3099, disk_mb=3099, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --alignEndsType EndToEnd --outFilterMismatchNoverLmax 0.05 --genomeDir /shareDB/genomes/Homo_sapiens/UCSC/hg38/Sequence/hg38_star_v2.7.10a_index --readFilesIn /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siTAZ/IY-siTAZ_R1.fastq.gz --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --twopassMode Basic --runThreadN 20 --sjdbGTFfile /home/labs/bioservices/services/ngs/support/gtf/hg38-gencode.genes.gtf --quantMode GeneCounts --readFilesCommand zcat --outFileNamePrefix /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IY-siTAZ --genomeLoad NoSharedMemory --sjdbGTFtagExonParentGene gene_name --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IY-siTAZ.txt 2>&1 export HOME=$HOME /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IY-siTAZAligned.sortedByCoord.out.bam >> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IY-siTAZ.txt 2>&1 [Mon Nov 18 23:10:49 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=3210, disk_mb=3210, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 23:02:41 2024] rule rule_3_mapping: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siTAZ/IZ-siTAZ_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IZ-siTAZAligned.sortedByCoord.out.bam log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IZ-siTAZ.txt jobid: 0 reason: Forced execution wildcards: sample=IZ-siTAZ threads: 20 resources: mem_mb=3210, disk_mb=3210, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --alignEndsType EndToEnd --outFilterMismatchNoverLmax 0.05 --genomeDir /shareDB/genomes/Homo_sapiens/UCSC/hg38/Sequence/hg38_star_v2.7.10a_index --readFilesIn /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siTAZ/IZ-siTAZ_R1.fastq.gz --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --twopassMode Basic --runThreadN 20 --sjdbGTFfile /home/labs/bioservices/services/ngs/support/gtf/hg38-gencode.genes.gtf --quantMode GeneCounts --readFilesCommand zcat --outFileNamePrefix /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IZ-siTAZ --genomeLoad NoSharedMemory --sjdbGTFtagExonParentGene gene_name --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IZ-siTAZ.txt 2>&1 export HOME=$HOME /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IZ-siTAZAligned.sortedByCoord.out.bam >> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IZ-siTAZ.txt 2>&1 [Mon Nov 18 23:10:56 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1404, disk_mb=1404, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 22:55:25 2024] rule rule_3_mapping: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siYAP/IQ-siYAP_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IQ-siYAPAligned.sortedByCoord.out.bam log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IQ-siYAP.txt jobid: 0 reason: Forced execution wildcards: sample=IQ-siYAP threads: 20 resources: mem_mb=1404, disk_mb=1404, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --alignEndsType EndToEnd --outFilterMismatchNoverLmax 0.05 --genomeDir /shareDB/genomes/Homo_sapiens/UCSC/hg38/Sequence/hg38_star_v2.7.10a_index --readFilesIn /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siYAP/IQ-siYAP_R1.fastq.gz --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --twopassMode Basic --runThreadN 20 --sjdbGTFfile /home/labs/bioservices/services/ngs/support/gtf/hg38-gencode.genes.gtf --quantMode GeneCounts --readFilesCommand zcat --outFileNamePrefix /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IQ-siYAP --genomeLoad NoSharedMemory --sjdbGTFtagExonParentGene gene_name --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IQ-siYAP.txt 2>&1 export HOME=$HOME /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IQ-siYAPAligned.sortedByCoord.out.bam >> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IQ-siYAP.txt 2>&1 [Mon Nov 18 23:02:37 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=5853, disk_mb=5853, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 23:05:13 2024] rule rule_3_mapping: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siYAP/IY-siYAP_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IY-siYAPAligned.sortedByCoord.out.bam log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IY-siYAP.txt jobid: 0 reason: Forced execution wildcards: sample=IY-siYAP threads: 20 resources: mem_mb=5853, disk_mb=5853, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --alignEndsType EndToEnd --outFilterMismatchNoverLmax 0.05 --genomeDir /shareDB/genomes/Homo_sapiens/UCSC/hg38/Sequence/hg38_star_v2.7.10a_index --readFilesIn /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siYAP/IY-siYAP_R1.fastq.gz --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --twopassMode Basic --runThreadN 20 --sjdbGTFfile /home/labs/bioservices/services/ngs/support/gtf/hg38-gencode.genes.gtf --quantMode GeneCounts --readFilesCommand zcat --outFileNamePrefix /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IY-siYAP --genomeLoad NoSharedMemory --sjdbGTFtagExonParentGene gene_name --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IY-siYAP.txt 2>&1 export HOME=$HOME /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IY-siYAPAligned.sortedByCoord.out.bam >> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IY-siYAP.txt 2>&1 [Mon Nov 18 23:14:29 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=2355, disk_mb=2355, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 22:57:06 2024] rule rule_3_mapping: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siYAP/IZ-siYAP_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IZ-siYAPAligned.sortedByCoord.out.bam log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IZ-siYAP.txt jobid: 0 reason: Forced execution wildcards: sample=IZ-siYAP threads: 20 resources: mem_mb=2355, disk_mb=2355, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --alignEndsType EndToEnd --outFilterMismatchNoverLmax 0.05 --genomeDir /shareDB/genomes/Homo_sapiens/UCSC/hg38/Sequence/hg38_star_v2.7.10a_index --readFilesIn /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siYAP/IZ-siYAP_R1.fastq.gz --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --twopassMode Basic --runThreadN 20 --sjdbGTFfile /home/labs/bioservices/services/ngs/support/gtf/hg38-gencode.genes.gtf --quantMode GeneCounts --readFilesCommand zcat --outFileNamePrefix /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IZ-siYAP --genomeLoad NoSharedMemory --sjdbGTFtagExonParentGene gene_name --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IZ-siYAP.txt 2>&1 export HOME=$HOME /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IZ-siYAPAligned.sortedByCoord.out.bam >> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IZ-siYAP.txt 2>&1 [Mon Nov 18 23:04:17 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1991, disk_mb=1991, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 22:55:55 2024] rule rule_3_mapping: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siC/IQ-siC_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IQ-siCAligned.sortedByCoord.out.bam log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IQ-siC.txt jobid: 0 reason: Forced execution wildcards: sample=IQ-siC threads: 20 resources: mem_mb=1991, disk_mb=1991, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --alignEndsType EndToEnd --outFilterMismatchNoverLmax 0.05 --genomeDir /shareDB/genomes/Homo_sapiens/UCSC/hg38/Sequence/hg38_star_v2.7.10a_index --readFilesIn /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siC/IQ-siC_R1.fastq.gz --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --twopassMode Basic --runThreadN 20 --sjdbGTFfile /home/labs/bioservices/services/ngs/support/gtf/hg38-gencode.genes.gtf --quantMode GeneCounts --readFilesCommand zcat --outFileNamePrefix /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IQ-siC --genomeLoad NoSharedMemory --sjdbGTFtagExonParentGene gene_name --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IQ-siC.txt 2>&1 export HOME=$HOME /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IQ-siCAligned.sortedByCoord.out.bam >> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IQ-siC.txt 2>&1 [Mon Nov 18 23:02:52 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=5283, disk_mb=5283, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 23:05:13 2024] rule rule_3_mapping: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siC/IY-siC_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IY-siCAligned.sortedByCoord.out.bam log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IY-siC.txt jobid: 0 reason: Forced execution wildcards: sample=IY-siC threads: 20 resources: mem_mb=5283, disk_mb=5283, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --alignEndsType EndToEnd --outFilterMismatchNoverLmax 0.05 --genomeDir /shareDB/genomes/Homo_sapiens/UCSC/hg38/Sequence/hg38_star_v2.7.10a_index --readFilesIn /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siC/IY-siC_R1.fastq.gz --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --twopassMode Basic --runThreadN 20 --sjdbGTFfile /home/labs/bioservices/services/ngs/support/gtf/hg38-gencode.genes.gtf --quantMode GeneCounts --readFilesCommand zcat --outFileNamePrefix /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IY-siC --genomeLoad NoSharedMemory --sjdbGTFtagExonParentGene gene_name --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IY-siC.txt 2>&1 export HOME=$HOME /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IY-siCAligned.sortedByCoord.out.bam >> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IY-siC.txt 2>&1 [Mon Nov 18 23:14:30 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] 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 23:09:49 2024] rule rule_2_multiQC: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IQ-siTAZ/IQ-siTAZ_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IY-siTAZ/IY-siTAZ_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IZ-siTAZ/IZ-siTAZ_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IQ-siYAP/IQ-siYAP_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IY-siYAP/IY-siYAP_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IZ-siYAP/IZ-siYAP_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IQ-siC/IQ-siC_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IY-siC/IY-siC_R1_fastqc/fastqc_data.txt, /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IZ-siC/IZ-siC_R1_fastqc/fastqc_data.txt output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/multiQC/multiqc_report.html log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_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/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/multiQC /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc &>/home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_multiQC.txt [Mon Nov 18 23:09:57 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1709, disk_mb=1709, mem_mb_per_thread=3000, mem_mb_total=60000 Select jobs to execute... [Mon Nov 18 22:56:47 2024] rule rule_3_mapping: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siC/IZ-siC_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IZ-siCAligned.sortedByCoord.out.bam log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IZ-siC.txt jobid: 0 reason: Forced execution wildcards: sample=IZ-siC threads: 20 resources: mem_mb=1709, disk_mb=1709, tmpdir=/tmp, mem_mb_per_thread=3000, mem_mb_total=60000 /opt/miniconda3/envs/utap/bin/STAR --alignEndsType EndToEnd --outFilterMismatchNoverLmax 0.05 --genomeDir /shareDB/genomes/Homo_sapiens/UCSC/hg38/Sequence/hg38_star_v2.7.10a_index --readFilesIn /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siC/IZ-siC_R1.fastq.gz --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --twopassMode Basic --runThreadN 20 --sjdbGTFfile /home/labs/bioservices/services/ngs/support/gtf/hg38-gencode.genes.gtf --quantMode GeneCounts --readFilesCommand zcat --outFileNamePrefix /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IZ-siC --genomeLoad NoSharedMemory --sjdbGTFtagExonParentGene gene_name --outSAMattributes NH HI AS nM MD > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IZ-siC.txt 2>&1 export HOME=$HOME /opt/miniconda3/envs/utap/bin/samtools index /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/3_mapping/IZ-siCAligned.sortedByCoord.out.bam >> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/3_mapping.IZ-siC.txt 2>&1 [Mon Nov 18 23:02:36 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=2690, disk_mb=2690, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Mon Nov 18 23:07:17 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siTAZ/IQ-siTAZ_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IQ-siTAZ/IQ-siTAZ_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IQ-siTAZ.txt jobid: 0 reason: Forced execution wildcards: sample=IQ-siTAZ threads: 5 resources: mem_mb=2690, disk_mb=2690, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IQ-siTAZ /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IQ-siTAZ -f fastq --threads 5 /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siTAZ/IQ-siTAZ_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IQ-siTAZ.txt 2>&1 [Mon Nov 18 23:09:25 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=2913, disk_mb=2913, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Mon Nov 18 22:53:56 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IQ-siTAZ/IQ-siTAZ_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siTAZ/IQ-siTAZ_R1.fastq.gz log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IQ-siTAZ.txt jobid: 0 reason: Forced execution wildcards: sample=IQ-siTAZ threads: 4 resources: mem_mb=2913, disk_mb=2913, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -a "T{10}" -j 4 --times 2 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siTAZ/IQ-siTAZ_R1.fastq.gz /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IQ-siTAZ/IQ-siTAZ_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siTAZ.cutadapt.txt 2> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IQ-siTAZ.txt && touch /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siTAZ/IQ-siTAZ_R1.fastq.gz.deleted [Mon Nov 18 22:56:11 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=3099, disk_mb=3099, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Mon Nov 18 23:05:37 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siTAZ/IY-siTAZ_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IY-siTAZ/IY-siTAZ_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IY-siTAZ.txt jobid: 0 reason: Forced execution wildcards: sample=IY-siTAZ threads: 5 resources: mem_mb=3099, disk_mb=3099, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IY-siTAZ /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IY-siTAZ -f fastq --threads 5 /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siTAZ/IY-siTAZ_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IY-siTAZ.txt 2>&1 [Mon Nov 18 23:08:05 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=3346, disk_mb=3346, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Mon Nov 18 22:53:59 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IY-siTAZ/IY-siTAZ_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siTAZ/IY-siTAZ_R1.fastq.gz log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IY-siTAZ.txt jobid: 0 reason: Forced execution wildcards: sample=IY-siTAZ threads: 4 resources: mem_mb=3346, disk_mb=3346, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -a "T{10}" -j 4 --times 2 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siTAZ/IY-siTAZ_R1.fastq.gz /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IY-siTAZ/IY-siTAZ_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siTAZ.cutadapt.txt 2> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IY-siTAZ.txt && touch /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IY-siTAZ/IY-siTAZ_R1.fastq.gz.deleted [Mon Nov 18 22:56:15 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=3210, disk_mb=3210, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Mon Nov 18 23:04:56 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siTAZ/IZ-siTAZ_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IZ-siTAZ/IZ-siTAZ_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IZ-siTAZ.txt jobid: 0 reason: Forced execution wildcards: sample=IZ-siTAZ threads: 5 resources: mem_mb=3210, disk_mb=3210, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IZ-siTAZ /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IZ-siTAZ -f fastq --threads 5 /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siTAZ/IZ-siTAZ_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IZ-siTAZ.txt 2>&1 [Mon Nov 18 23:07:31 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Provided resources: mem_mb=3467, disk_mb=3467, mem_mb_per_thread=125, mem_mb_total=500 Select jobs to execute... [Mon Nov 18 22:53:59 2024] rule rule_1_cutadapt: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IZ-siTAZ/IZ-siTAZ_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siTAZ/IZ-siTAZ_R1.fastq.gz log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IZ-siTAZ.txt jobid: 0 reason: Forced execution wildcards: sample=IZ-siTAZ threads: 4 resources: mem_mb=3467, disk_mb=3467, tmpdir=/tmp, mem_mb_per_thread=125, mem_mb_total=500, runtime=02:30 /opt/miniconda3/envs/utap/bin/cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{10}" -a "T{10}" -j 4 --times 2 -q 20 -m 25 -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siTAZ/IZ-siTAZ_R1.fastq.gz /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/0_concatenating_fastq/IZ-siTAZ/IZ-siTAZ_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siTAZ.cutadapt.txt 2> /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/1_cutadapt.IZ-siTAZ.txt && touch /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IZ-siTAZ/IZ-siTAZ_R1.fastq.gz.deleted [Mon Nov 18 22:56:23 2024] Finished job 0. 1 of 1 steps (100%) done All samples:['IZ-siYAP', 'IQ-siC', 'IZ-siC', 'IY-siC', 'IQ-siTAZ', 'IQ-siYAP', 'IY-siTAZ', 'IY-siYAP', 'IZ-siTAZ'] factors:['siTAZ', 'siTAZ', 'siTAZ', 'siYAP', 'siYAP', 'siYAP', 'siC', 'siC', 'siC'] deseq samples:['IQ-siTAZ', 'IY-siTAZ', 'IZ-siTAZ', 'IQ-siYAP', 'IY-siYAP', 'IZ-siYAP', 'IQ-siC', 'IY-siC', 'IZ-siC'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 5 Rules claiming more threads will be scaled down. Provided resources: mem_mb=1404, disk_mb=1404, mem_mb_per_thread=800, mem_mb_total=4000 Select jobs to execute... [Mon Nov 18 23:06:49 2024] rule rule_2_fastqc: input: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siYAP/IQ-siYAP_R1.fastq.gz output: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IQ-siYAP/IQ-siYAP_R1_fastqc/fastqc_data.txt log: /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IQ-siYAP.txt jobid: 0 reason: Forced execution wildcards: sample=IQ-siYAP threads: 5 resources: mem_mb=1404, disk_mb=1404, tmpdir=/tmp, mem_mb_per_thread=800, mem_mb_total=4000 mkdir -p /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IQ-siYAP /opt/miniconda3/envs/utap/bin/fastqc --extract -o /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/2_fastqc/IQ-siYAP -f fastq --threads 5 /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/1_cutadapt/IQ-siYAP/IQ-siYAP_R1.fastq.gz > /home/labs/bioservices/Collaboration/exmaple_and_data_for_testing_hg38_RNA-seq/20241118_225254_data_for_demo_production_Transcriptome_RNA-Seq/logs_20241118_225254/2_fastqc.IQ-siYAP.txt 2>&1 [Mon Nov 18 23:07:59 2024] Finished job 0. 1 of 1 steps (100%) done