Can't convert multiple SAMs from SRA to BAMs
Hey everyone, I am trying to download some SAM files from SRA and pipe them into samtools view. However, with three files I get an error:
sam-dump was killed (signal 9 SIGKILL)
[E::sam_parse1] SEQ and QUAL are of different length
[W::sam_read1_sam] Parse error at line 9647365
samtools view: error reading file "-": Inappropriate ioctl for device
Is there something wrong with the files or is my command wrong?
(sam-dump [Accession] | samtools view -b -o [Accession].bam) &> [Accession].log
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gernophil •
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seems like a problem with the data file itself. if you provide the accession number others could try to verify your issue
Hey there, one accession number would be: SRR5134861
Make sure you are using a reasonably latest version of
samtools.I am using samtools 1.15.1. Still running into this error.
@GenoMax: Did you execute the command above? What's the
-at the end of your command? You left out the-bflag. Is that automatically detected when defining a bam output file?Yes the output format is automatically detected by
samtoolsbased on file name extension.-at the end of the command is for input coming from the piped output ofsam-dump. I used the same version of samtools.That's weird. I am gonna try your syntax next week, when I'm back. Even though I don't see, why it should make a difference. Didn't know the
-syntax for piping, so thanks for that :). The weird thing is, that it works with most files, but it consistently fails on three files. I am running this on a slurm cluster. Maybe this is the problem here.