PASA- seqclean error

[Reema Singh]

Hello Everybody,

My apologies for the duplicate post. But, I thought might be I get some suggestion on Trinity google group. Please see my query:- 

I am trying to run seqclean, but getting following error :- 

"ERROR: psx: child terminated with nonzero exit status (1) - exiting!!

WAITING for all children to finish before exiting!

Error at 'psx -p 1  -n 1000  -i good.NewAssembly_31259.fasta -d cleaning -C '/homes/rsingh/TranscriptAssembly/Dicty-Genome/Dicty-Trinity/PASA_Annotation/Pasa_Dicty_Alt_Parameter_WO_SeqCenter/PASA_Trinity_good/good.NewAssembly_31259.fasta:ANLMS100:/homes/rsingh/TranscriptAssembly/Dicty-Genome/Dicty-Trinity/PASA_Annotation/Pasa_Dicty_Alt_Parameter_WO_SeqCenter/PASA_Trinity_good/dgca_kovector.fasta::11:0' -c '/cluster/gjb_lab/software/centos6.3/opt/PASA-2.0.1/seqclean/seqclean/bin/seqclean.psx''

Process terminated with an error! "

The the command I am using is "seqclean good.NewAssembly_31259.fasta -v dgca_kovector.fasta". I used the same command before to clean the sequences and it works.

I though it must be the "seqclean.psx" permission problem. But the same command without vector sequence works fine [ seqclean good.NewAssembly_31259.fasta]. I have no idea what's happening here."

Any suggestion would be very helpful.

Many Thanks,

Reema,

[Brian Haas]

If seqclean is giving you trouble, I'd suggest just skipping it.  It's nonessential, though helpful if you do get it to work with some fiddling.  Best support I can give right now, unfortunately.

-Brian

(by iPhone)

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[Daren Card]

I ran into an error like this as well, and it is indeed a permissions issue. The permissions I observed on these files were:

$ ls -lh /usr/local/bin/PASApipeline-2.0.2/seqclean/seqclean/bin/

total 428K

-rwxrwxr-x 1 1597    61 111K Jul 13  2004 cdbfasta

-rwxrwxr-x 1 1597    61 110K Jul 13  2004 cdbyank

-rwxrwxr-x 1 1597    61 8.5K Apr  9  2003 mdust

-rwxrwxr-x 1 1597    61  13K Apr  9  2003 psx

-rwxrwxr-x 1 1597    61 146K Apr  9  2003 pvmsx

-rwxr-x--x 1 1418 games  12K Jul 13  2004 seqclean.psx

-rwxrwxr-x 1 1597    61  15K Apr  9  2003 trimpoly

So I just changed the file ownerships using a command like this:

$ sudo chown user:group /usr/local/bin/PASApipeline-2.0.2/seqclean/seqclean/bin/*

This appears to have fixed this issue. Maybe not the best solution, but no solution I ever come up with is.

Hope that helps.

Daren

[Brian Haas]

Works for me!  Thanks!  :)

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas