[maker-devel] ipr_update_gff ERROR

[Carson Holt]

This error would happen if some results exist in the iprscan output, but
don't match gene entries in the GFF3 file.  If I could see the original
files I can tell you which ones.  This can happen if you combine results
from the non-overlapping.fasta files with the maker.proteins.fasta files for
example.  Models in the non-overlapping.fasta file are not genes in the GFF3
(they are match/match_part enties), so errors happen.

Thanks,
Carson

From:  p sz <seoanezonjic at hotmail.com>
Date:  Tuesday, 22 May, 2012 8:55 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] ipr_update_gff ERROR

First, thanks by help me on the lprevious error that I submitted.
I'm still working in the same project and I get a new error. I try
interproscan with this commandline:

iprscan_wrap -i parsed_input.all.maker.proteins.fasta -email
seoanezonjic at hotmail.com  -format raw

parsed_input.all.maker.proteins.fasta was generated with the tool
fasta_merge. I use the output (attached in this email) and a gff file
(generated by a normal run of maker, attached in this email) with the
ipr_update_gff script of this way:

ipr_update_gff BAC12_Clone_Pt314B2_Lib_Pt_7Ba__organism_Pinus_taeda__0.gff
sc_interpro.sh.o109053

And i get this error:
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 1.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 2.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 3.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 8.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 9.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 10.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 11.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 12.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 13.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 14.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 179, <$IN> line 15.
Use of uninitialized value $gene_id in hash element at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 181, <$IN> line 15.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 18.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 18.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 18.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 19.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 19.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 19.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 48.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 48.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 48.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 49.
Use of uninitialized value in string eq at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 69, <$IN> line 49.
Use of uninitialized value in concatenation (.) or string at
/export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff
line 70, <$IN> line 49.

The gff file seems updated but i don't know if it works fine or is corrupt
Thanks in advance
       
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