Question

Error while conversion of .sam to sorted.sam using samtools

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10.5 years ago

Mohit ▴ 30

Hey hi,

I have used BWA for the alignment purpose. The .sam files are obtained after BWA step. I have converted it to .bam

Now I want to sort the .bam file to get .sorted.bam for this I have used command:

~admin1/software/samtools-0.1.19/samtools sort xyz.bam xyz.sorted

But some Error is coming:-->

"[bam_sort_core] truncated file. Continue anyway."

Thanking you for consideration!!!

Mohit R. Navandar

ChIP-Seq • 4.3k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 10.5 years ago by Mohit ▴ 30

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The BWA output (.sam) may not be complete or it might be corrupt file.. Is it the case?

ADD REPLY • link updated 3.2 years ago by Ram 44k • written 10.5 years ago by Mohit ▴ 30

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The SAM file is probably fine. The BAM file, on the other hand, is probably where the problem is.

ADD REPLY • link 10.5 years ago by Devon Ryan 105k

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Try

samtools sort

single threaded, that is, without -@

Based on 960 BAMs that failed with this error multithreaded, but succeeded single-threaded, I strongly suspect a bug in the samtools threading code.

(samtools ver. 1.2, on Linux)

ADD REPLY • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by artg • 0

score 2 · Answer 1 · 2014-06-20

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10.5 years ago

Devon Ryan 105k

The original file was corrupt or otherwise incomplete. Just remake the BAM file.

ADD COMMENT • link 10.5 years ago by Devon Ryan 105k