panic: bam: magic number mismatch about goleft

[shenwei356]

It said

indexQGP/0100004781_S2_L002.sorted.bam.bai: no such file or directory

That means, you should create index for the bam file using samtools index.

[snashraf]

Sorry for mistake last time. I have updated question again.

[brentp]

It would be nice if this were a better message, but an incorrectly formatted bam is a panic. Can you make sure to update to the latest goleft? The problem will likely perisist, but it would be good to verify.

I would first try running ls -lhS on your bams and see if any are very small or outliers. If that fails, you can run it on half your samples at a time--doing a binary search to find the problematic bam or bai.

[brentp]

I am closing this for lack of activity. please reopen if you can help narrow it down or recreate.