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-t/--threads cmd line parsing error #56

@cmatKhan

Description

@cmatKhan

. I am using v0.5.5, and originally submitted with the following cmd:

ngm \
      -r KN99_genome_fungidb.fasta \
      -q run_1272_s_3_withindex_sequence_AAATGCA.fastq.gz \
      --threads 2 \
      --bam

but, I received this error:

/usr/local/bin/ngm-core: unrecognized option '--threads'

The help text says --threads is a valid argument:

...
General:

 -t/--threads <int>            Number of candidate search threads
...

I resubmitted, replacing --threads with -t and eliminated that error:

  ngm \
     -r KN99_genome_fungidb.fasta \
     -q run_1272_s_3_withindex_sequence_AAATGCA.fastq.gz \
     -t 2 \
     --bam 

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