[BiO BB] Re: Gene ontology PDB files & InterproScan query
Dr Nicky Mulder
nmulder at science.uct.ac.za
Thu Nov 16 12:28:32 EST 2006
>
>
>------------------------------
>
>Message: 3
>Date: Tue, 14 Nov 2006 12:32:36 -0600
>From: kannaiah at bsd.uchicago.edu
>Subject: [BiO BB] InterProscan XML output error
>To: bio_bulletin_board at bioinformatics.org
>Message-ID: <1163529156.455a0bc409e46 at netmail.bsd.uchicago.edu>
>Content-Type: text/plain; charset=ISO-8859-1
>
>Hello,
>
>Anybody here use Interproscan anytime?
>If so, I am wondering if you ever ran into an error like this: An xml output error.
>
>Not sure whats going wrong here:(. Any ideas?
>
>Thank you.
>
>-----------------------------------------------------
>[root at cccluster iprscan]# /clusta/shah/local_progs/iprscan/bin/iprscan -cli
>-appl hmmsmart -appl hmmpfam -i /clusta/shah/local_progs/iprscan/test.seq -o
>/clusta/shah/local_progs/iprscan/test.out
>SUBMITTED iprscan-20061114-12101842
>
>FAILED
> Iprscan job iprscan-20061114-12101842 failed and exit with status code 256
>/clusta/shah/local_progs/iprscan/bin/iprscan:
>/clusta/shah/local_progs/iprscan/tmp/20061114/iprscan-20061114-12101842/iprscan-20061114-12101842.xml
>unavailable : No such file or directory
>/clusta/shah/local_progs/iprscan/bin/iprscan_wrapper.pl: failed to send error to
>administrator: no destination address
>Tool: iprscan
>JobID: iprscan-20061114-12101842
>Time: Tue Nov 14 12:11:37 2006
>Error:
>
>supervise: doRawResults: failed to create XML output :
>
>Job submission parameters:
>DD 14
>MM 11
>YYYY 2006
>appl hmmsmart,hmmpfam
>cmd submit
>crc 1
>format xml
>frame 6
>hh 12
>jobid iprscan-20061114-12101842
>mm 10
>nseqs 3
>onego 1
>remotehost cccluster.uchicago.cc
>seq.1.1.crc64 F94D07049A6D489D
>seq.1.1.id RS16_ECOLI
>seq.1.1.len 82
>seq.1.2.crc64 D44DAE8C544CB7C1
>seq.1.2.id Q9RHD9
>seq.1.2.len 267
>seq.1.3.crc64 CD84A335CCFFE6D7
>seq.1.3.id Y902_MYCTU
>seq.1.3.len 446
>seqtype P
>srchtype interactive
>ss 18
>submission cli
>tool iprscan
>
>NOTE: the newlines have been replaced with backslash.
>----------------------------------------------------------
>
>
>
>
You should send this query direclty to interhelp at ebi.ac.uk, who can help.
>Message: 4
>Date: Wed, 15 Nov 2006 12:41:13 +0000 (GMT)
>From: Ulisses Dias <ulimard at yahoo.com.br>
>Subject: [BiO BB] Gene ontology PDB files
>To: "General Forum at Bioinformatics.Org"
> <bio_bulletin_board at bioinformatics.org>
>Message-ID: <20061115124114.10256.qmail at web56613.mail.re3.yahoo.com>
>Content-Type: text/plain; charset=iso-8859-1
>
>Hi!
>
> Anyone knows how can I get the PDB numbers for all the genes products associated to a GO term?
>
>Thank you
> Ulisses Dias
>
>
>
The GOA database provides a file of PDB to GO annotations, see this page
of downloades:
http://www.ebi.ac.uk/GOA/downloads.html
See the readme file for more info on the PDB GO annotations
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