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Old 01-31-2015, 07:37 PM   #1
sandesh
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Location: TN

Join Date: Jun 2013
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Default parallel blat (pblat) error

Hello all,

I found modified blat for parallel running, which has -threads option.
But getting error:

blat Pcap_genome.2bit test-protein.fasta -t=dnax -q=prot -mask=lower test_blat -out=blast8 -threads=2

Loaded 64023748 letters in 827 sequences
Blatx 827 sequences in database, 750 files in query
not found

Anybody happen to have this issue.
Please any solution?

Thanks
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Old 03-04-2016, 07:07 AM   #2
Macspider
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Default Similar problem

Actually I don't have an answer, but I can add some evidence of the problem. To me, it happens that after loading the sequences it quits the job without standard errors, and the .psl output file contains nothing but the header.

Did you find any solution during this year of work? (I see the date of your post, I hope you had )
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Old 03-09-2016, 05:41 AM   #3
Macspider
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Default

I think I have an answer to your question, even though it comes 1 year after and you probably found out by yourself.

As far as I know, blat and pblat accept this kind of input:
blat database query [options] output.psl

In your case, the threads are specified after the output.psl file, and this is why it prints out not found at the end: it doesn't find any correspondance to that option, probably.

I can also add some troubleshooting about pblat that could help anybody who reads this post. The reason why pblat doesn't output anything was that the version of pblat I was using did not support the list mode of input read files. This means that if I provided a list of fasta files to align as it was possible to do in blat, the program didn't recognize that file as a valid one, and aligned nothing.

Finally, another troubleshooting solved: pblat, if compiled with the intel/15.*.* compiler, runs but yields an error in generating the output file if the full path is given. This error is due to some programming errors probably, that are fixed in the most recent version, but if you have the older one you can turn around this obstacle by giving a local path and not the full one.

Hope this helps someone! To me, it meant part of my phd project!
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