getAllChromosomesBed fails with KeyError: 'HLA-A*01'

[stfacc]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v1.10.1-g79ddc44

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-human-variation --bam /home/sfacchini/mnt/rd013s/230813_Andrea_WGS_analysis/bam/61552/61552.bam --ref /data/array/sfacchini/wf-human-variation_test/Homo_sapiens_assembly38.fasta --sample_name sample_61552 --snp --sv --cnv --str --phased --sv_benchmark --threads 64

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

Workflow does not complete.

Relevant log output

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'getAllChromosomesBed (1)'

Caused by:
  Process `getAllChromosomesBed (1)` terminated with an error exit status (1)

Command executed:

  faidx --transform bed Homo_sapiens_assembly38.fasta > allChromosomes.bed

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/home/epi2melabs/conda/bin/faidx", line 10, in 
      sys.exit(main())
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/pyfaidx/cli.py", line 202, in main
      write_sequence(args)
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/pyfaidx/cli.py", line 51, in write_sequence
      outfile.write(transform_sequence(args, fasta, name, start, end))
    File "/home/epi2melabs/conda/lib/python3.8/site-packages/pyfaidx/cli.py", line 121, in transform_sequence
      line_len = fasta.faidx.index[name].lenc
  KeyError: 'HLA-A*01'

Work dir:
  /data/array/sfacchini/wf-human-variation_test/work/ef/666925c42764353af4683d525c4f8c

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

[vlshesketh]

Hi @stfacc thank you for reporting this! We will investigate a fix and update when it's released.

[vlshesketh]

Hi @stfacc, this has been fixed in v1.11.0 which we have just released. Thank you for using wf-human-variation, and please let us know if you have any further issues.