Error: "Searching alignments... No such file or directory"

[mirandaccarter]

Hi, I'm trying to run diamond on a file and it appears I get about halfway through before this error gets thrown. I'm not sure why this would be happening, because I've run several other files (some much larger in size) from the same sequencing run without issue, but this file has errored out twice now. Thanks in advance!

This is the last chunk in the log file:

Processing query block 1, reference block 54/137, shape 1/2, index chunk 2/4.
Building reference seed array... [2.17s]
Building query seed array... [0.444s]
Computing hash join... [0.783s]
Masking low complexity seeds... [0.142s]
Searching alignments... No such file or directory
No such file or directory
No such file or directory
No such file or directory
terminate called after throwing an instance of 'terminate called recursively
terminate called recursively
terminate called recursively
/tmp/slurmd/job51687827/slurm_script: line 26: 3962009 Aborted (core dumped)

My code:

diamond blastx
--query SQK-RBK114-96_barcode19.fastq
--db nr.dmnd
--out SQK-RBK114-96_barcode19.daa
-F 15
-f 100
--range-culling
--top 10 \

[bbuchfink]

Try to use the option --no-unlink.

[mirandaccarter]

That worked! Thank you! Just out of curiosity, is there a reason why this one file out of 30 would require that addition when every other file had no issues?

[bbuchfink]

No idea but you need not worry, that option does not change the results.