Hi. I a running this pipeline with multiple samples and I am getting an error with mirtop. This is the error message I get:

ERROR ~ Error executing process > 'NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MIRNA_MIRTOP:MIRTOP_GFF (IGtrES_12)'

Caused by:
  Process `NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MIRNA_MIRTOP:MIRTOP_GFF (IGtrES_12)` terminated with an error exit status (1)


Command executed:

  mirtop \
      gff \
       \
      --sps dre \
      --hairpin hairpin.fa_igenome.fa_idx.fa \
      --gtf dre.gff3 \
      -o mirtop \
      IGtrES_12.bam
  
  mv mirtop/mirtop.gff mirtop/IGtrES_12_mirtop.gff
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MIRNA_MIRTOP:MIRTOP_GFF":
      mirtop: $(echo $(mirtop --version 2>&1) | sed 's/^.*mirtop //')
  END_VERSIONS

Command exit status:
  1

Command output:
  ['gff', '--sps', 'dre', '--hairpin', 'hairpin.fa_igenome.fa_idx.fa', '--gtf', 'dre.gff3', '-o', 'mirtop', 'IGtrES_12.bam']

Command error:
  /opt/conda/lib/python3.12/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
    warnings.warn(
  03/11/2013 05:55:15 INFO Run annotation
  03/11/2013 05:55:15 ERROR Database not found in --mirna dre.gff3. Use --database argument to add a custom source.
  Traceback (most recent call last):
    File "/opt/conda/bin/mirtop", line 10, in <module>
      sys.exit(main())
               ^^^^^^
    File "/opt/conda/lib/python3.12/site-packages/mirtop/command_line.py", line 31, in main
      reader(kwargs["args"])
    File "/opt/conda/lib/python3.12/site-packages/mirtop/gff/__init__.py", line 24, in reader
      database = mapper.guess_database(args)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.12/site-packages/mirtop/mirna/mapper.py", line 23, in guess_database
      return _guess_database_file(args.gtf, args.database)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.12/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 dre.gff3 header

Work dir:
  /share/data05/gthemudo/a2s/ignition/mirna/data/transport/work/75/3a71a11eaf4ab49607740860af8b07

Container:
  /share/data05/gthemudo/a2s/ignition/mirna/data/transport/work/singularity/community.wave.seqera.io-library-mirtop_pybedtools_pysam_samtools_pruned-60b8208f3dbb2910.img

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`

 -- Check '.nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details

In the work directory there is a dre.gff3 file that is not empty. So I am not sure why it is throwing an error.

Have a look at https://github.com/nf-core/smrnaseq/issues/329 and https://github.com/nf-core/smrnaseq/issues/284. Maybe there is a solution, or at least you have a better idea why it doesn't work. 🤞

Hi. I solved this error by using an older version (2.3.1) of the pipeline (after reading https://github.com/nf-core/smrnaseq/issues/284). I then got another error with the bowtie index. I think it is because my reference genome is gzipped and the pipeline is not identifying that. I am building the index now outside the pipeline to see if that works instead.