GroopM error

[pbravakos]

GroopM exits with an error message. When I run the following command:

python2 groopm2 parse --threads 20 \
                                 --cutoff 500 \
                                 --force \
                                 db.gm \
                                 OSD100_MegaHIT_KrakenUniqNoCont.fasta \
                                 BamPESample2.bam \
                                 BamPESample2.bam \
                                 BamPESample3.bam \
                                 BamPESample4.bam \
                                 BamPESample5.bam \
                                 BamPESample6.bam

I get the following error:

Mapping contigs
Error creating database: OSD100_MegaHIT_GroopM_db.gm <class 'subprocess.CalledProcessError'>
Unexpected error: <class 'subprocess.CalledProcessError'>
Traceback (most recent call last):
  File "/home1/pbravakos/Software/GroopM/bin/groopm2", line 669, in <module>
    args.run(args)
  File "/home1/pbravakos/Software/GroopM/bin/groopm2", line 189, in __call__
    threads=options.threads)
  File "/home1/pbravakos/.local/lib/python2.7/site-packages/groopm/data3.py", line 340, in createDB
    (contig_indices, marker_indices, marker_names, marker_counts, taxstrings) = mapper.getMappings(contigsFile, cid_2_indices)
  File "/home1/pbravakos/.local/lib/python2.7/site-packages/groopm/data3.py", line 1862, in getMappings
    (con_indices, map_markers, map_taxstrings) = self._runMapper(contig_file, cid_2_indices, self._mode, working_directory)
  File "/home1/pbravakos/.local/lib/python2.7/site-packages/groopm/data3.py", line 1845, in _runMapper
    return mapper.getMappings(contig_file, cid_2_indices)
  File "/home1/pbravakos/.local/lib/python2.7/site-packages/groopm/map.py", line 83, in getMappings
    subprocess.check_call(cmd, shell=True)
  File "/usr/lib/python2.7/subprocess.py", line 186, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'singlem pipe --sequences /mnt/scratch/pbravakos/OSD/KrakenUniq/OSD100/OSD100_MegaHIT_KrakenUniqNoCont.fasta --archive_otu_table /tmp/tmpMVNVUn/singlem_otu_table.cs
v 2> /dev/null' returned non-zero exit status 1

If I change the command above to use graftM then I get a new error:

Mapping contigs
Error creating database: OSD100_MegaHIT_GroopM_db.gm <class 'subprocess.CalledProcessError'>
Unexpected error: <class 'subprocess.CalledProcessError'>
Traceback (most recent call last):
  File "/home1/pbravakos/Software/GroopM/bin/groopm2", line 669, in <module>
    args.run(args)
  File "/home1/pbravakos/Software/GroopM/bin/groopm2", line 189, in __call__
    threads=options.threads)
  File "/home1/pbravakos/.local/lib/python2.7/site-packages/groopm/data3.py", line 340, in createDB
    (contig_indices, marker_indices, marker_names, marker_counts, taxstrings) = mapper.getMappings(contigsFile, cid_2_indices)
  File "/home1/pbravakos/.local/lib/python2.7/site-packages/groopm/data3.py", line 1862, in getMappings
    (con_indices, map_markers, map_taxstrings) = self._runMapper(contig_file, cid_2_indices, self._mode, working_directory)
  File "/home1/pbravakos/.local/lib/python2.7/site-packages/groopm/data3.py", line 1845, in _runMapper
    return mapper.getMappings(contig_file, cid_2_indices)
  File "/home1/pbravakos/.local/lib/python2.7/site-packages/groopm/map.py", line 161, in getMappings
    read_tax_files = dict([self.mapPackage(contigFile, package) for package in self.packageList])
  File "/home1/pbravakos/.local/lib/python2.7/site-packages/groopm/map.py", line 209, in mapPackage
    subprocess.check_call(cmd, shell=True)
  File "/usr/lib/python2.7/subprocess.py", line 186, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'graftM graft --forward /mnt/scratch/pbravakos/OSD/KrakenUniq/OSD100/OSD100_MegaHIT_KrakenUniqNoCont.fasta --graftm_package /home1/pbravakos/Software/graftm_gpkgs/7
.71.silva_v132_alpha1.gpkg --output_directory /tmp/tmptjP3Nq/OSD100_MegaHIT_KrakenUniqNoCont_7.71.silva_v132_alpha1 --verbosity 2 2> /dev/null' returned non-zero exit status 1

Both singleM and graftM seem to be installed properly. Do you have any idea on how I can run GroopM without any errors?