KeyError 'gene_id' in salmon_tx2gene.py

[didillysquat]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/rnaseq pipeline documentation

Description of the bug

The salmon_tx2gene.py script is throwing an error of

Traceback (most recent call last):
    File "/home/humebc/.nextflow/assets/nf-core/rnaseq/bin/salmon_tx2gene.py", line 88, in <module>
      tx2gene(args.gtf, args.salmon, args.id, args.extra, args.output)
    File "/home/humebc/.nextflow/assets/nf-core/rnaseq/bin/salmon_tx2gene.py", line 47, in tx2gene
      gene_dict[attr_dict[gene_id]].append(attr_dict)
  KeyError: 'gene_id'

This is being caused due to the fact that the "gene_id" key is not present in the key-value pairings of the .gtf file being used as input. This is only the case for a small number of the lines. For the majority, "gene_id" is present. I originally gave your pipeline a GFF file as input. The GFF file is this one: GCF_017654675.1_Xenopus_laevis_v10.1_genomic.gff.gz.

The offending line in the salmon_tx2gene.py is this one:

gene_dict[attr_dict[gene_id]].append(attr_dict)

Because the "gene_id" key is present in the vast majority of the lines, this line can be surrounded in a try: except: and the script will complete with no issue. E.g.:

try:
    gene_dict[attr_dict[gene_id]].append(attr_dict)
except KeyError:
    continue

Alternatively, i suppose this problem could be fixed in the part of the workflow that is responsible for converting the GFF file into a .gtf file by ensuring that every output line has a "gene_id" key value pairing.

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line:

nextflow -c nextflow.config.heim run nf-core/rnaseq --input /home/humebc/projects/20211102_heim/nf_rna_seq/heim_sample_sheet.csv --pseudo_aligner salmon --transcript_fasta /home/humebc/projects/20211102_heim/xenopus_references/GCF_017654675.1_Xenopus_laevis_v10.1_rna.fna.gz --salmon_index /home/h
umebc/projects/20211102_heim/xenopus_references/xenopus.gentrome.index -profile docker --fasta /home/humebc/projects/20211102_heim/xenopus_references/GCF_017654675.1_Xenopus_laevis_v10.1_genomic.fna.gz --gff /home/humebc/projects/20211102_heim/xenopus_references/GCF_017654675.1_Xenopus_laevis_v10.1_genomic.gff.gz

2. See error:
   See above

Expected behaviour

I would expect the script to complete and produce the salmon_tx2gene.tsv.

nextflow.log

Log files

Have you provided the following extra information/files:

• The command used to run the pipeline
• The .nextflow.log file

System

• Hardware:
  linux server
• Executor:
• OS:
  linux ubuntu
• Version
  v3.3

Nextflow Installation

• Version:
  21.04.1.5556

Container engine

• Engine:
  -Docker
• version:
• Docker version 20.10.5, build 55c4c88

Additional context

[drpatelh]

Added the try logic in 9c0641a @didillysquat.

The other option of checking during the conversion will be trickier I suppose because we are using GFFREAD to do that and not a custom script. If you can find a solution with that then we can try and add it but patched for now based on your initial suggestion.

Will close for now but feel free to re-open if things change. Cheers!

[didillysquat]

Great. Thanks @drpatelh !