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fail to locate the index #244

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wbsimey opened this issue Jul 3, 2019 · 0 comments
Open

fail to locate the index #244

wbsimey opened this issue Jul 3, 2019 · 0 comments

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@wbsimey
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wbsimey commented Jul 3, 2019

Hello, we created an index with:
'bwa index -p Tse_SBAPGDGG -a bwtsw Tse_SBAPGDGG.fa'
It completed in about an hour (genome is 2.4Gbp).
it created the following files in the same dir:
483K Jul 2 15:13 Tse_SBAPGDGG.amb
1.9M Jul 2 15:13 Tse_SBAPGDGG.ann
2.2G Jul 2 15:13 Tse_SBAPGDGG.bwt
543M Jul 2 15:13 Tse_SBAPGDGG.pac
1.1G Jul 2 15:42 Tse_SBAPGDGG.sa

then we ran from same dir:
'bwa aln -n 0.04 -M 3 -R 35 -O 6 -E 2 -t 16 Tse_SBAPGDGG.fa TP29750_HS2500_L001_R1.fastq.gz > bwa.sai/TP29750_HS2500_L001_R1.sai >> logfile'
and we get:
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln] fail to locate the index
I have bwa.sai and bwa.sam dirs in this dir.ls -lh
What have we done wrong?

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