blastx generates empty output file

Question

[dovi]

I am trying to run blastx (version 2.2.28) with the following command line:

blastx -db nr -outfmt 5 -evalue 1e-3 -word_size 3 -show_gis -num_alignments 1 \
-max_hsps 20 -num_threads 5 -out transcripts_refonly.xml -query transcripts_refonly.fa

So when blastx is running, I can see the output file that grows in size, however when blastx finishes, the output file then is empty (0kb). This happens when I run it with big files like transcprit fasta file (from a RNA-seq project) of ~30Mb (21000 sequences), but if I run just a smaller file (20 sequences) it works good.

I tried also with .txt ouput format and it happens the same, and also run it into the cluster and different servers and still not working.

Does someone knows what I am doing wrong?

Thank you

[GenoMax]

Sounds like you are running out of space (or hitting some limit on storage quota). Have you looked into those possibilities?

[dovi]

It does not seem to be a space problem... I have about 853TiB in my workspace in the cluster. When I run it in the server I had about 30GB (with no limit), do you think it will need that amount?

[GenoMax]

If you are sure that there are no storage quota then this is not making sense. And this happens reproducibly? If you are starting multiple jobs you are using unique outfile names for each job (example above seems generic but it may just be an example)?

[dovi]

yes, my outfile names are unique for each job

Answer 1

[dovi]

I guess that it was something about memory.. still don't know. My solution: just split my file into several small files (~100 sequences per file) and run multiple blastx at the same time in the cluster.

[GenoMax]

Out of curiosity: what is the average size of the output files for these small jobs? What was the size you saw the original file grow to with the full dataset?

[dovi]

The size of the output file (xml) obtained with the small jobs is 300Kb on average while the file size from the big blastx job was more than 3Mb, but it is just an estimation because at the end of the job the file was empty

[GenoMax]

Guess the cause will have to remain a mystery since the file sizes are comparatively tiny.