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Mapping Issue #3

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zeliy90 opened this issue Jun 25, 2020 · 0 comments
Open

Mapping Issue #3

zeliy90 opened this issue Jun 25, 2020 · 0 comments

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@zeliy90
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zeliy90 commented Jun 25, 2020

Hi everytime I run pangia I get this error message when its trying to map my reads could you tell me why?

[ERROR] error occurred while running read mapping (code: 1, message: + bwa mem -k40 -T60 -h100 -B2 -t24 database/NCBI_genomes_refseq89_BAV.fa SRR172902.fastq

  • gawk '-F\t' '!/^@/ { print }'
  • gawk '-F\t' '!and($2,256) && !and($2,2048) { print } END { print NR > "./SRR172902_tmp/raw_sam/NCBI_genomes_refseq89_BAV.fa.sam.count" }'
  • gawk '-F\t' '!and($2,4) { print }'
    ).
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