[maker-devel] iprscan and ipr_update_gff

[kdelmore at zoology.ubc.ca]

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_174837921_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_174837921_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_210353293_gsjh
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