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stampy "stuck" aligning

Hi all,

I am using stampy for aligning against a reference genome but it seems to get stuck during the alignment process. For a single sorted.bam file, it will produce alignments for ~ 3mn and then does not produce anything. It says it is aligning but no more data are being produced, even after running my script for 12 hours. Here is what I tried:

  • Reinstall stampy and reindex the genome
  • Tried with different genome versions
  • Tried with different sorted.bam files (including some that previously worked to align with stampy)

None of this helped.

Maybe it needs more time but I find it strange it is taking so long particularly for a sorted.bam file that is just 10MB. My sorted.bam files are from a BWA alignment, samtools view to create the .bam files and samtools sort to sort them.

Any thoughts or ideas are welcome!

stampy alignment
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written by AP AP

2 answers

Have you previously run stampy successfully, what version of stampy are you using, how large is your reference genome, how much computer memory do you have available?

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written by mastal511 mastal511

Hi, - Yes I did run stampy successfully in the past. - The version I am using is 1.0.28 with Python version 2.7.10. - My genome size is about 450 million bp - I have lots of computer power: currently running my jobs on a HPC. I am usually running stampy for max 12 hrs with 1CPU and 12 computational nodes (which should be more than enough). Currently trying again running it for 24hrs but so far still stuck.

Any thoughts would be much appreciated!

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written by AP AP

Problem solved: samtools 1.3 was sorting the files in a weird fashion causing stampy to crash. Switching back to version 1.2 solved the problem.

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written by AP AP

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