[maker-devel] iprscan and ipr_update_gff

[Carson Holt]

You have entries in your interproscan output that aren't in your GFF3.  Is
your GFF3 file truncated?

--Carson


On 5/5/14, 10:36 PM, "kdelmore at zoology.ubc.ca" <kdelmore at zoology.ubc.ca>
wrote:

>Hi, I have a question about the interproscan scripts available with maker.
>
>I'm following the recommendations posted by Carson in Aug 2011 to
>incorporate results from iprscan. I'm getting quite a few warning messages
>with ipr_update_gff; they're all the same and suggest that there's no
>value for $name. When I look through the updated gff, however, the dbxrefs
>have been added. Is this something I should be worried about?
>
>I'm using iprscan version 5 and actually get some warning messages there
>as well but again, the output looks alright. In addition, some of my
>fastas don't get these warnings in iprscan and they still give me the
>error with ipr_update_gff so I don't think that's the problem. I'm using
>proteins from UniProt. My commands and errors are below. I've also
>attached the first 20000 lines from my initial gff and raw file from
>iprscan.
>
>Thanks, I really appreciate your continued support.
>Kira
>
>###
>
>commands for interproscan scripts available in maker
>iprscan2gff3 6.maker.proteins.fasta.xml.raw 6.gff  > 6.domains.gff
>gff3_merge 6.gff 6.domains.gff -o 6_w_domains.all.gff
>ipr_update_gff 6_w_domains.all.gff 6.maker.proteins.fasta.xml.raw -inplace
>
>error after last step (just an example, a ton of similar lines):
>Use of uninitialized value $name in hash element at
>/home/kdelmore/tools/maker/bin/ipr_update_gff line 107, <$IN> line 15242.
>Use of uninitialized value $name in hash element at
>/home/kdelmore/tools/maker/bin/ipr_update_gff line 107, <$IN> line 15353.
>Use of uninitialized value $name in hash element at
>/home/kdelmore/tools/maker/bin/ipr_update_gff line 107, <$IN> line 15674.
>Use of uninitialized value $name in hash element at
>/home/kdelmore/tools/maker/bin/ipr_update_gff line 107, <$IN> line 15776.
>
>
>###
>
>commands for interproscan 5
>interproscan.sh -i 6.maker.proteins.fasta -f xml -goterms -iprlookup \ >
>interpro_6.out 2>&1
>interproscan.sh -mode convert -f raw -i 6.maker.proteins.fasta.xml
>
>error after first step:
>04/05/2014 19:22:09:269 25% completed
>04/05/2014 21:27:36:305 50% completed
>04/05/2014 21:32:34:236 75% completed
>04/05/2014 21:38:01:379 90% completed
>2014-05-04 21:50:22,761
>[uk.ac.ebi.interpro.scan.management.model.implementations.WriteOutputStep:
>248]
>WARN - At run completion, unable to delete temporary directory
>/lustre/home/kdelmore/interpro_good/interpro_6/temp/cl2n116_20140504_17483
>7921_l959/jobPIRSF-2.84
>2014-05-04 21:50:22,908
>[uk.ac.ebi.interpro.scan.management.model.implementations.WriteOutputStep:
>253]
>WARN - At run completion, unable to delete temporary directory
>/lustre/home/kdelmore/interpro_good/interpro_6/temp/cl2n116_20140504_17483
>7921_l959
>04/05/2014 21:50:23:380 100% done:  InterProScan analyses completed
>
>error after second step:
>interproscan.sh -mode convert -f raw -i 6.maker.proteins.fasta.xml
>05/05/2014 21:03:40:457 Welcome to InterProScan-5.3-46.0
>05/05/2014 21:03:53:292 Running InterProScan v5 in CONVERT mode...
>2014-05-05 21:04:00,603
>[uk.ac.ebi.interpro.scan.jms.converter.Converter:277] WARN - At run
>completion, unable to delete temporary directory
>/home/kdelmore/interpro_good/interpro_6/temp/jasper.westgrid.ca_20140505_2
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