mirTop error, Database not found in --mirna hsa.gff3. Use --database argument to add a custom source.

[mdozmorov]

Description of the bug

This error still occurs in 2.2.3. It appears to have a fix, when running the pipeline with -r fix-mirtop-gff (using fix-mirtop-gff branch), the pipeline completes. Would be good to have it in the main branch, for reproducibility. Shortened message:

ERROR ~ Error executing process > 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:MIRTOP_QUANT'

Caused by:
  Process `NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:MIRTOP_QUANT` terminated with an error exit status (1)
...
Command error:
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  /usr/local/lib/python3.9/site-packages/mirtop/mirna/mintplates.py:512: SyntaxWarning: "is" with a literal. Did you mean "=="?
    if prefix is '':
  09/10/2023 09:09:02 INFO Run annotation
  09/10/2023 09:09:02 ERROR Database not found in --mirna hsa.gff3. Use --database argument to add a custom source.
  Traceback (most recent call last):
    File "/usr/local/bin/mirtop", line 10, in <module>
      sys.exit(main())
    File "/usr/local/lib/python3.9/site-packages/mirtop/command_line.py", line 31, in main
      reader(kwargs["args"])
    File "/usr/local/lib/python3.9/site-packages/mirtop/gff/__init__.py", line 24, in reader
      database = mapper.guess_database(args)
    File "/usr/local/lib/python3.9/site-packages/mirtop/mirna/mapper.py", line 23, in guess_database
      return _guess_database_file(args.gtf, args.database)
    File "/usr/local/lib/python3.9/site-packages/mirtop/mirna/mapper.py", line 40, in _guess_database_file
      raise ValueError("Database not found in %s header" % gff)
  ValueError: Database not found in hsa.gff3 header

Command used and terminal output

nextflow run nf-core/smrnaseq --input ${INPUT} \
  --outdir ${DIROUT} \
  -profile 'singularity' \
  --genome GRCh38 \
  --mirtrace_species 'hsa' \
  --protocol 'illumina' \
  --skip_mirdeep \
  -resume
#  -r fix-mirtop-gff # Using this fixes the problem

Relevant files

No response

System information

nextflow version 23.04.3.5875, HPC, local, singularity, CentOS 7, 2.2.3

[yangfeizZZ]

Hello, I wonder if you have solved this error. I met the same error.

[shepp-hub]

I can confirm that the issue persists.

[christopher-mohr]

I can confirm that the issue persists.

Hi @shepp-hub, could you please check if the issue still exists with the latest release 2.3.0.

[christopher-mohr]

Please reopen if the problem persists.