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[M::bwa_idx_load_from_disk] read 0 ALT contigs #412

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erah1 opened this issue Mar 13, 2024 · 0 comments
Open

[M::bwa_idx_load_from_disk] read 0 ALT contigs #412

erah1 opened this issue Mar 13, 2024 · 0 comments

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@erah1
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erah1 commented Mar 13, 2024

I am trying to map exome capture reads against a genome using BWA and I received the following error message

[M::bwa_idx_load_from_disk] read 0 ALT contigs
_R1_val_1.fq.gz'.l to open file `/path/to/trimmed/reads/sample1

My command was:

bwa index -a bwtsw reference.fasta
bwa mem -t 32 reference.fasta sample1_R1_val_1.fq.gz sample1_R2_val_2.fq.gz > sample1.sam
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@erah1