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Hey everyone! a complete newbie here. I am runnin...
# help
m
Hey everyone! a complete newbie here. I am running the pipeline (for chipSeq) on my local PC and keep getting warning saying "[b5/15bd9f] NOTE: Process 
BWA_MEM (sample name)
terminated with an error exit status (137) -- Execution is retried (1)" with every sample being procced until the pipeline stops and produce an error with different exit status (sometimes 137, sometimes 1..)I suspected that it might be computer resources (memory issues??) but my SDD has 40 GB (out of 240 GB) free. Any idea on what might be causing this error? I would be very happy to provide with any further info, code....etc many thanks for any input 🙂
j
moreinfo
s
To help we'd love a few more details please: 1. The Nextflow command you used to launch the pipeline 2. Any custom Nextflow config files 3. The full error message 4. The corresponding 
.nextflow.log
file, where you are running the analysis. Remember to use triple backslashes on their own lines for code blocks. Also take a look at https://nf-co.re/usage/troubleshooting for more information on debugging failed pipelines. Thanks!
m
For sure! the error text: Error executing process > 'BWA_MEM (ENCSR000EEN_R1_T1)' Caused by: Process 
BWA_MEM (ENCSR000EEN_R1_T1)
terminated with an error exit status (137) Command executed: bwa mem \ -t 4 \ -M \ -R '@RG\tIDENCSR000EEN R1 T1\tSMENCSR000EEN_R1\tPLILLUMINA\tLBENCSR000EEN_R1_T1\tPU:1' \ \ BWAIndex/GRCh38.p13.genome.fa \ ENCSR000EEN_R1_T1_trimmed.fq.gz \ | samtools view -@ 4 -b -h -F 0x0100 -O BAM -o ENCSR000EEN_R1_T1.Lb.bam - Command exit status: 137 Command output: (empty) Command error: [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 1126704 sequences (40000038 bp)... [M::process] read 1126784 sequences (40000006 bp)... .command.sh: line 9: 27 Killed bwa mem -t 4 -M -R '@RG\tIDENCSR000EEN R1 T1\tSMENCSR000EEN_R1\tPLILLUMINA\tLBENCSR000EEN_R1_T1\tPU:1' BWAIndex/GRCh38.p13.genome.fa ENCSR000EEN_R1_T1_trimmed.fq.gz 29 Done | samtools view -@ 4 -b -h -F 0x0100 -O BAM -o ENCSR000EEN_R1_T1.Lb.bam - Work dir: /home/sam/practice_clone/CLASS_2023/CLASSES/03_Nextflow/test-chip/work/a6/91c0c96709fd22a99d4e85400461c5 Tip: view the complete command output by changing to the process work dir and entering the command 
cat .command.out
the progress before the error:executor > local (8) [6c/f0b7ae] process > CHECK_DESIGN (design.csv) [100%] 1 of 1, cached: 1 ✔️ [9d/a50afa] process > BWA_INDEX (GRCh38.p13.genome.fa) [100%] 1 of 1, cached: 1 ✔️ [4f/0ab222] process > MAKE_GENE_BED (gencode.v32.annotation.gtf) [100%] 1 of 1, cached: 1 ✔️ [80/258767] process > MAKE_GENOME_FILTER (GRCh38.p13.genome.fa) [100%] 1 of 1, cached: 1 ✔️ [5b/24b802] process > FASTQC (POLR2A_R4_T1) [100%] 6 of 6, cached: 6 ✔️ executor > local (8) [6c/f0b7ae] process > CHECK_DESIGN (design.csv) [100%] 1 of 1, cached: 1 ✔️ [9d/a50afa] process > BWA_INDEX (GRCh38.p13.genome.fa) [100%] 1 of 1, cached: 1 ✔️ [4f/0ab222] process > MAKE_GENE_BED (gencode.v32.annotation.gtf) [100%] 1 of 1, cached: 1 ✔️ [80/258767] process > MAKE_GENOME_FILTER (GRCh38.p13.genome.fa) [100%] 1 of 1, cached: 1 ✔️ [5b/24b802] process > FASTQC (POLR2A_R4_T1) [100%] 6 of 6, cached: 6 ✔️ [53/2eaf42] process > TRIMGALORE (ENCSR000EEN_R1_T1) [100%] 6 of 6, cached: 6 ✔️ [a6/91c0c9] process > BWA_MEM (ENCSR000EEN_R1_T1) [ 63%] 7 of 11, cached: 1, failed: 6, retries: 5 [64/5f6067] process > SORT_BAM (POLR2A_R2_T1) [100%] 1 of 1, cached: 1 [- ] process > MERGED_BAM - [- ] process > MERGED_BAM_FILTER - [- ] process > PRESEQ - [- ] process > PICARD_METRICS - [- ] process > BIGWIG - [- ] process > PLOTPROFILE - [- ] process > PHANTOMPEAKQUALTOOLS - [- ] process > PLOTFINGERPRINT - [- ] process > MACS2 - [- ] process > MACS2_ANNOTATE - [- ] process > MACS2_QC - [- ] process > CONSENSUS_PEAKS - [- ] process > CONSENSUS_PEAKS_ANNOTATE - [- ] process > CONSENSUS_PEAKS_COUNTS - [- ] process > CONSENSUS_PEAKS_DESEQ2 - [- ] process > IGV - [c1/41a1c3] process > get_software_versions [100%] 1 of 1 ✔️ [- ] process > MULTIQC - [e1/47fd42] process > output_documentation [100%] 1 of 1, cached: 1 ✔️
the nextflow.config: process { executor = 'local' // Use 'local' for running on your own computer memory = '6 GB' // Adjust memory based on your computer's capacity maxForks = 2 // Set a lower number of forks to avoid overloading your CPU } process { withName: 'BWA_INDEX' { cpus = 4 } } process { withName: 'MAKE_GENE_BED' { memory = '6 GB' } } process { withName: 'CHECK_DESIGN' { memory = '6 GB' } } process { withName: 'BWA_INDEX' { memory = '6 GB' } } params { max_memory = '6 GB' max_cpus = 4 } trace { overwrite = true } process { withName: 'BWA_MEM' { memory = '6 GB' cpus = 4 } }
j
You're running out of memory, i.e. RAM (not harddrive space!)
resourcehelp
s
You likely need to configure the pipeline to your available computational resources to you machine or infrastructure. Please see the following two(!) sections: - https://nf-co.re/docs/usage/getting_started/configuration#tuning-workflow-resources - https://nf-co.re/docs/usage/getting_started/configuration#max-resources of the documentation for more information.
m
Thanks James! I will read through these two docs
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