Nextflow workflow report

[marvelous_pesquet]

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 127.

The full error message was:

Error executing process > 'SNPS:freebayes (sample1)'

Caused by:
  Process `SNPS:freebayes (sample1)` terminated with an error exit status (127)

Command executed:

  fasta_generate_regions.py genome.fa.fai 100000 > regions.txt
  freebayes-parallel regions.txt 16 -f genome.fa sample1.bam \
  --no-partial-observations --report-genotype-likelihood-max --genotype-qualities --min-repeat-entropy 1 --min-coverage 10 > sample1.vcf

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 2: fasta_generate_regions.py: command not found

Work dir:
  /home/shared/8TB_HDD_01/sr320/github/paper-oly-mbdbs-gen/work/61/4d759a0808789724d69e6d78aab137

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Run times
20-Jun-2022 10:47:35 - 16-Nov-2022 11:50:42 (duration: 149d 2h 3m 6s)
  30 succeeded  
  0 cached  
  0 ignored  
  12 failed  
Nextflow command
nextflow run epidiverse/snp -profile test, docker
CPU-Hours
0.4 (0% failed)
Launch directory
/home/shared/8TB_HDD_01/sr320/github/paper-oly-mbdbs-gen
Work directory
/home/shared/8TB_HDD_01/sr320/github/paper-oly-mbdbs-gen/work
Project directory
/home/sr320/.nextflow/assets/epidiverse/snp
Script name
main.nf
Script ID
b0e299ed332648922c66d8a020a05bca
Workflow session
2ed67bda-48aa-4cb2-905a-a864344acfa8
Workflow repository
https://github.com/EpiDiverse/snp.git, revision master (commit hash 9c814703c690c2ade21c4586b36159940e092a4e)
Workflow profile
test,
Nextflow version
version 20.07.1, build 5412 (24-07-2020 15:18 UTC)

Resource Usage

These plots give an overview of the distribution of resource usage for each process.

CPU

Memory

Job Duration

I/O

Tasks

This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.

(tasks table omitted because the dataset is too big)