[maker-devel] iprscan and ipr_update_gff

[kdelmore at zoology.ubc.ca]

Thanks for your reply. I have not truncated the gff3. I'm using files from
the datastore that were written at the same time so I'm not sure how that
would happen. I split my multifasta before running it through maker and
have not merged the gff or protein.fasta for iprscan. That wouldn't be the
problem would it?

> 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
>>10353293_gsjh_______________________________________________
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>
>
>