Strainphlan.py won't run when additional arguments are passed

[Megan Folkerts]

Hello,

I'm running an installation of strainphlan that I downloaded from the bitbucket repository to by-pass the current issue with conda download. When I run strainphlan.py with minimal arguments as follows:

strainphlan.py --ifn_samples samplemarkersout/*.markers --ifn_markers s_B_intestinihominis.markers.fasta --ifn_ref_genomes /scratch/mfolkerts/bin/ncbi-genomes-2019-12-20/GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna --output_dir relaxed_parameters/ --clades s__Barnesiella_intestinihominis --nprocs_main 8 --mpa_pkl /scratch/mfolkerts/bin/metaphlan_databases/mpa_v294_CHOCOPhlAn_201901.pkl

everything runs correctly, and RaXML trees are created. However when I try to run with relaxed parameters like so:

strainphlan.py --ifn_samples samplemarkersout/*.markers --ifn_markers s_B_intestinihominis.markers.fasta --ifn_ref_genomes /scratch/mfolkerts/bin/ncbi-genomes-2019-12-20/GCF_000296465.1_Barn_inte_YIT_11860_V1_genomic.fna --output_dir relaxed_parameters/ --clades s__Barnesiella_intestinihominis --nprocs_main 8 --relaxed_parameters --mpa_pkl /scratch/mfolkerts/bin/metaphlan_databases/mpa_v294_CHOCOPhlAn_201901.pkl 

I get the following error:

Traceback (most recent call last):

  File "/scratch/mfolkerts/bin/metaphlan/strainphlan.py", line 1583, in <module>

    strainphlan()

  File "/scratch/mfolkerts/bin/metaphlan/strainphlan.py", line 1579, in strainphlan

    strainer(args)

  File "/scratch/mfolkerts/bin/metaphlan/strainphlan.py", line 1512, in strainer

    float(clade2num_markers[c]) < args['marker_in_clade']:

UnboundLocalError: local variable 'c' referenced before assignment

I'm also getting this error, if, instead of using --relaxed_parameters, I manually pass any or all arguments that --relaxed_parameters conveys. Do you have any idea why this might be happening or what I can do to fix it? 

Thanks,

Megan

[Aitor Blanco-Miguez]

Hi Megan,
Could you check which version of the MetaPhlAn2.9 database did you use for executing sample2markers Script?
On your previous post you were using the version v2.95 for extracting the markers from your metagenomic samples. If this is the case, can you try to execute StrainPhlAn with the v2.95 database version?

Best,

Aitor

[Megan Folkerts]

I will try 2.95. I was using 2.94, as there was that issue with the viral genomes in 2.95. 

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Megan Folkerts, MS
Research Associate II
Center for Emerging Pathogens and Technologies
TGen North
Flagstaff, Arizona
928-226-6375

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[Megan Folkerts]

That fixed it. Thank you!