BWA2 command error
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22 months ago
waik • 0

I commanded

$BWA2 mem -t 1 -R "@RG\tID:sample\tSM:sample\tPL:platform" ../resource/reference/hg38.chr21.fa sample_1.fastq.gz sample_2.fastq.gz > sample.mapped.sam

but there was error

bash: mem: command not found

I tried to find solutions. but no clues.

FASTA BWA2 • 563 views
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Make sure the $BWA2 bash variable is set with echo $BWA2.

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and use simple quotes for option -R , otherwise, tabs will be expanded in the SAM header which can break some programs.

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