Can't convert multiple SAMs from SRA to BAMs

Question

[gernophil]

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

[cmdcolin]

seems like a problem with the data file itself. if you provide the accession number others could try to verify your issue

[gernophil]

Hey there, one accession number would be: SRR5134861

[GenoMax]

$ sam-dump SRR5134861 | samtools view -o test.bam -

Make sure you are using a reasonably latest version of samtools.

[gernophil]

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 -b flag. Is that automatically detected when defining a bam output file?

[GenoMax]

Yes the output format is automatically detected by samtools based on file name extension. - at the end of the command is for input coming from the piped output of sam-dump. I used the same version of samtools.

[gernophil]

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.