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MDU-PHL / ngmaster

In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)
GNU General Public License v3.0
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ngmaster fails when mincov or minid flags are used #39

Open kapsakcj opened 1 year ago

kapsakcj commented 1 year ago

Installed ngmaster 1.0.0 via bioconda using mamba:

# create conda env
$ mamba create -n ngmaster -c conda-forge -c bioconda -c defaults ngmaster

# activate env
$ mamba activate ngmaster

# test runs successfully
$ ngmaster --test
Running ngmaster.py on test example (NG-MAST 4186 / NG-STAR 231) ...
FILE    SCHEME  NG-MAST/NG-STAR porB_NG-MAST    tbpB    penA    mtrR    porB_NG-STAR    ponA    gyrA    parC    23S
/home/curtis_kapsak/miniconda3/envs/ngmaster/lib/python3.9/site-packages/ngmaster/test/test.fa  ngmaSTar        4186/231        2569    241     23      42       100     100     10      2       100
... Test successful.

# runs successfully on a N. gonnorhoeae genome
$ ngmaster contigs.fasta 
FILE    SCHEME  NG-MAST/NG-STAR porB_NG-MAST    tbpB    penA    mtrR    porB_NG-STAR    ponA    gyrA    parC    23S
contigs.fasta       ngmaSTar        19265/2050      11156   362     23      19      4       1       100     2       100

# fails upon adding --minid
$ ngmaster --minid 85 contigs.fasta 
Command '['/home/curtis_kapsak/miniconda3/envs/ngmaster/bin/mlst', '--legacy', '-q', '--threads', '16', '--datadir', '/home/curtis_kapsak/miniconda3/envs/ngmaster/lib/python3.9/site-packages/ngmaster/db/pubmlst', '--blastdb', '/home/curtis_kapsak/miniconda3/envs/ngmaster/lib/python3.9/site-packages/ngmaster/db/blast/mlst.fa', '--scheme', 'ngmast', '--minid', "['85']", '--mincov', '10', 'contigs.fasta']' returned non-zero exit status 1.

# fails upon adding --mincov
$ ngmaster --mincov 15 contigs.fasta 
Command '['/home/curtis_kapsak/miniconda3/envs/ngmaster/bin/mlst', '--legacy', '-q', '--threads', '16', '--datadir', '/home/curtis_kapsak/miniconda3/envs/ngmaster/lib/python3.9/site-packages/ngmaster/db/pubmlst', '--blastdb', '/home/curtis_kapsak/miniconda3/envs/ngmaster/lib/python3.9/site-packages/ngmaster/db/blast/mlst.fa', '--scheme', 'ngmast', '--minid', '95', '--mincov', "['15']", 'contigs.fasta']' returned non-zero exit status 1.

# if I run the mlst cmd presented in the error, it runs successfully?
$ /home/curtis_kapsak/miniconda3/envs/ngmaster/bin/mlst --legacy -q --threads 16 --datadir /home/curtis_kapsak/miniconda3/envs/ngmaster/lib/python3.9/site-packages/ngmaster/db/pubmlst --blastdb /home/curtis_kapsak/miniconda3/envs/ngmaster/lib/python3.9/site-packages/ngmaster/db/blast/mlst.fa --scheme ngmast --minid 95 --mincov 15 contigs.fasta
FILE    SCHEME  ST      porB    tbpB
Warning: [blastn] Number of threads was reduced to 8 to match the number of available CPUs
contigs.fasta       ngmast  19265   11156   362

# exit code is 0 for mlst command
$ echo $?
0

I've also installed ngmaster via pip and encountered the same issue too, so I think the issue is something specific to taking in those 2 optional inputs

Am I doing something wrong here?