[maker-devel] iprscan and ipr_update_gff

[Carson Holt]

The file you sent was missing the ##FASTA entry and all sequence at the
bottom for example. Is that the way it is in the datastore?

--Carson


On 5/6/14, 9:06 AM, "kdelmore at zoology.ubc.ca" <kdelmore at zoology.ubc.ca>
wrote:

>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.WriteOutputSte
>>>p:
>>>248]
>>>WARN - At run completion, unable to delete temporary directory
>>>/lustre/home/kdelmore/interpro_good/interpro_6/temp/cl2n116_20140504_174
>>>83
>>>7921_l959/jobPIRSF-2.84
>>>2014-05-04 21:50:22,908
>>>[uk.ac.ebi.interpro.scan.management.model.implementations.WriteOutputSte
>>>p:
>>>253]
>>>WARN - At run completion, unable to delete temporary directory
>>>/lustre/home/kdelmore/interpro_good/interpro_6/temp/cl2n116_20140504_174
>>>83
>>>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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>>
>>
>>
>
>