Getting this error when running bwa-mem

1 
samtools sort: failed writing to "/var/tmp/samtools.18.2128.tmp.0000.bam": Inappropriate ioctl for device

and

Fatal error: Exit code 1 ()

It runs for a bit then this pops up, Im very new to using galaxy tools or sequencing.

Created a paired collection from two fastq files and ran fastp on them, and then bwa-mem on the output. Ive deleted the original fastq files to save space.

Tried an older version of bwa-mem and it seems to crash as well

[M::mem_pestat] low and high boundaries for proper pairs: (1, 635)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (49, 86, 128)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 286)
[M::mem_pestat] mean and std.dev: (84.60, 52.07)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 365)
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (110, 150, 204)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 392)
[M::mem_pestat] mean and std.dev: (159.38, 66.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 486)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[E::bgzf_flush] File write failed (wrong size)
[E::bgzf_close] File write failed
[E::bgzf_flush] File write failed (wrong size)
[E::bgzf_flush] File write failed (wrong size)
[E::bgzf_close] File write failed
[E::bgzf_close] File write failed
[E::bgzf_flush] File write failed (wrong size)
[E::bgzf_flush] File write failed (wrong size)
2

Hi @dna2026

You’ve posted another question on the forum about low coverage in bwa_mem2 alignments. Have you resolved the issue?

If not, have you done any QC after trimming? Check read names in both files to be sure the reads are properly paired. If the cause of the error is still unclear, share your history (you can post the URL into reply), so, people can check what is going on. History sharing: click at History options (three horizontal bars icon), select Share and Manage Access, in the middle window change Make history accessible to Yes, copy the URL and paste into reply.

Kind regards,

Igor

3

Thank you ! I have managed to run BWA MEM now - started from scratch on the EU galaxy servers, not sure if space was an issue before or me messing around with deleting some history files but it did run.

Still would need to solve the other question about coverage, though it’s a bit more complicated one !

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