SamtoolsError

[ikaufhold]

Hello,

thank you for developing this great tool! I am currently trying to use TEcount, but I am getting the following error:

[E::bgzf_flush] File write failed (wrong size)
Error occurred when reading first line of sample file /base/3.results/hisat2/GAGA-0177_worker_sorted.bam.
Error: 'samtools returned with error 1: stdout=, stderr=[bam_sort_core] merging from 31 files and 1 in-memory blocks...\nsamtools sort: failed writing to ".1717522536.691841.bam": Disk quota exceeded\n' 
[Exception type: SamtoolsError, raised in utils.py:69]

My bam files are sorted by position and I use the --sortByPos argument in the TEcount command. I already saw that other users resolved similar errors by re-sorting their bam files by name and removing the --sortByPos argument. The strange thing is, though, that for some of my samples, TEcount showed no error and ran smoothly, even though I use the exact same SAMtools and TEcount scripts for all of them. Could there maybe be another reason for this error?

Best regards, Isabell

[olivertam]

Hi,

Thank you for your interest in the software. It looks like you ran out of disk space during the initial sorting step. I don't know if you were running multiple TEcount at once, but it does need some space for re-sorting if you use the --sortByPos parameter. You could check that you still have sufficient space (approximately the amount used by the original BAM file) and clear up the space. You could also run TEcount one at a time if you don't have enough space for multiple BAM files to be re-sorted.

Thanks.

[ikaufhold]

Hi,

I cleared up some space, and it is working now, as long as I don't run too many jobs simultaneously. Thank you very much for your help!

All the best, Isabell