subprocess.CalledProcessError: while running GroopM2

[michaelwoodworth]

Hi, thanks for your hard work in developing and maintaining singleM. I'm working with GroopM2 and it is calling singlem and I'm getting this error:

Overwriting database groopm2_databases/SD01_database.gm                                                                                
Parsing contigs                                                                                                                        
Parsing BAM files using 1 threads                                                                                                      
Parsing file: /home/mwoodwo/prj/PREMIX/mg/17.groopm2/noncatreads_v_relabeled_concatenated_scaffolds/SD01-0419001.bam                   
Parsing file: /home/mwoodwo/prj/PREMIX/mg/17.groopm2/noncatreads_v_relabeled_concatenated_scaffolds/SD01-0419002.bam                   
Parsing file: /home/mwoodwo/prj/PREMIX/mg/17.groopm2/noncatreads_v_relabeled_concatenated_scaffolds/SD01-0419003.bam                   
Parsing file: /home/mwoodwo/prj/PREMIX/mg/17.groopm2/noncatreads_v_relabeled_concatenated_scaffolds/SD01-0718001.bam                   
Parsing file: /home/mwoodwo/prj/PREMIX/mg/17.groopm2/noncatreads_v_relabeled_concatenated_scaffolds/SD01-0818001.bam                   
Parsing file: /home/mwoodwo/prj/PREMIX/mg/17.groopm2/noncatreads_v_relabeled_concatenated_scaffolds/SD01-0818002.bam                   
Mapping contigs                                                                                                                        
Error creating database: groopm2_databases/SD01_database.gm <class 'subprocess.CalledProcessError'>                                    
Unexpected error: <class 'subprocess.CalledProcessError'>                                                                              
Traceback (most recent call last):                                                                                                     
  File "/home/mwoodwo/anaconda3/envs/groopm2/bin/groopm2", line 669, in <module>                                                       
    args.run(args)                                                                                                                     
  File "/home/mwoodwo/anaconda3/envs/groopm2/bin/groopm2", line 189, in __call__                                                       
    threads=options.threads)                                                                                                           
  File "/home/mwoodwo/anaconda3/envs/groopm2/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 "/home/mwoodwo/anaconda3/envs/groopm2/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 "/home/mwoodwo/anaconda3/envs/groopm2/lib/python2.7/site-packages/groopm/data3.py", line 1845, in _runMapper                    
    return mapper.getMappings(contig_file, cid_2_indices)                                                                              
  File "/home/mwoodwo/anaconda3/envs/groopm2/lib/python2.7/site-packages/groopm/map.py", line 83, in getMappings                       
    subprocess.check_call(cmd, shell=True)                                                                                             
  File "/home/mwoodwo/anaconda3/envs/groopm2/lib/python2.7/subprocess.py", line 190, in check_call                                     
    raise CalledProcessError(retcode, cmd)                                                                                             
subprocess.CalledProcessError: Command 'singlem pipe --sequences /home/mwoodwo/prj/PREMIX/mg/17.groopm2/relabeled_renamed_scaffolds/SD01
cat_scaffolds.fasta --archive_otu_table /tmp/tmpDd80UO/singlem_otu_table.csv 2> /dev/null' returned non-zero exit status 1  

Is this a familiar error or do you have suggestions on how to resolve it for singleM?

thanks!

Mike