samtools markdup

Question

[PROFESOR]

I'm doing deduplicate reads on a merged bam file, and I get this error

What is going on? What is the solution?

(base) javier@iMac-de-JAVIER BWA % samtools markdup -r -S 1merged.bam 2merged.bam

[tmp_file] Error: tmp file write data failed.
[markdup] error: writing temp output failed.
[E::bgzf_close] File write failed
[markdup] error closing output file
(base) javier@iMac-de-JAVIER BWA %

[aw7]

Well that is interesting, two errors that I have never seen before. So markdup cannot write to the temp file it made (needed when the -S option is used) and separately markdup cannot close the output file it made.

I suspect some problem with your file system. Can you write files to that directory with other programs?

[PROFESOR]

I think so, but I'm not sure, a few days ago I created a file with nano, but I didn't run it.

[PROFESOR]

It generates me as soon as the file begins, but with 0 bits

Answer 1

[PROFESOR]

It seems that it was due to lack of space on the disk, I have already done it, and I am doing a quality control, to see what results it gives

[Mensur Dlakic]

Exactly. It seems that you don't have enough disk space in the directory where temporary files are written.

[aw7]

samtools markdup will write temp files to the working directory unless you tell it otherwise with the -T option. I think all the samtools commands work like that (those that use temporary files).