mirTop error, Database not found in --mirna hsa.gff3. Use --database argument to add a custom source. #284
Description
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 problemRelevant files
No response
System information
nextflow version 23.04.3.5875, HPC, local, singularity, CentOS 7, 2.2.3