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. 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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