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samtools sort doesn't finish sorting bam file, just hangs for hours

I am trying to sort a bam file, which is 4.1 GB in size using simply samtools sort -o sorted.bam start.bam, but the file hangs after about 6.5 hours when the sorted file is 3.1 GB, no warning messages or anything. None of the temp files have been deleted either. I don't think the computer ran out of RAM. This has happened on my second attempt.

Why can't I sort this bam file? How can I get the sort to finish?

samtools
• 3,817 views • link
written by dec986 dec986

Very odd. Command seems fine. If you want to try a different tool use sambamba.

• 1 views • link
written by Jeffin Rockey Jeffin Rockey

Use top to see if the process is still running.

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written by ATpoint ATpoint

I don't think the computer ran out of RAM.

How much RAM do you have?

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written by GenoMax GenoMax

1 answer

Check 1 : is your BAM file okay? see below link

How to systematically check if a bam file is truncated

Check 2 : do you have enough space on disk ?

df -h
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written by lakhujanivijay lakhujanivijay

indeed, the issue was disk space, silly me. It would have been nice had samtools provided an error, however, the temp files used more space than I anticipated.

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written by dec986 dec986

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
Upvote|Bookmark|Accept

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written by WouterDeCoster WouterDeCoster

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