<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>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.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> p sz <<a href="mailto:seoanezonjic@hotmail.com">seoanezonjic@hotmail.com</a>><br><span style="font-weight:bold">Date: </span> Tuesday, 22 May, 2012 8:55 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] ipr_update_gff ERROR<br></div><div><br></div><div><style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Tahoma
}
--></style><div class="hmmessage"><div dir="ltr">
First, thanks by help me on the lprevious error that I submitted.<br>I'm still working in the same project and I get a new error. I try interproscan with this commandline:<br><br>iprscan_wrap -i parsed_input.all.maker.proteins.fasta -email <a href="mailto:seoanezonjic@hotmail.com">seoanezonjic@hotmail.com</a> -format raw<br><br>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:<br><br>ipr_update_gff BAC12_Clone_Pt314B2_Lib_Pt_7Ba__organism_Pinus_taeda__0.gff sc_interpro.sh.o109053<br><br>And i get this error:<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>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.<br>Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 18.<br>Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 18.<br>Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 18.<br>Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 18.<br>Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 19.<br>Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 19.<br>Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 19.<br>Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 19.<br>Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 48.<br>Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 48.<br>Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 48.<br>Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 48.<br>Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 49.<br>Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 49.<br>Use of uninitialized value in string eq at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 69, <$IN> line 49.<br>Use of uninitialized value in concatenation (.) or string at /export/home_users/home/soft/maker/programs/x86_64/maker/bin/ipr_update_gff line 70, <$IN> line 49.<br><br>The gff file seems updated but i don't know if it works fine or is corrupt<br>Thanks in advance<br> </div></div></div>_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a>
</span></body></html>