From frommer at cebitec.uni-bielefeld.de Fri Jun 21 08:57:30 2019 From: frommer at cebitec.uni-bielefeld.de (Bianca Frommer) Date: Fri, 21 Jun 2019 15:57:30 +0200 Subject: [maker-devel] substr outside of string at Carp.pm Message-ID: <4d5aded5-7458-39a8-2507-34ab34d6ce42@cebitec.uni-bielefeld.de> Dear support team, I ran MAKER successfully to generate data for training SNAP. However, now I want to run the training round with MAKER (run MAKER with the hmm file), but MAKER fails for every contig it processed till now. The "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the gff header line) and the error massage is attached below. I can not figure out what the problem is. Thank you! Sincerely, Bianca gathering ab-init output files deleted:0 genes substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line 346. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Calling translate without a seq argument! STACK: Error::throw STACK: Bio::Root::Root::throw /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447 STACK: Bio::Tools::CodonTable::translate /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419 STACK: CGL::TranslationMachine::longest_translation_plus_stop /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280 STACK: maker::auto_annotator::get_translation_seq /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236 STACK: Widget::snap::load_phat_hits /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974 STACK: Widget::snap::parse /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690 STACK: GI::parse_abinit_file /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194 STACK: Process::MpiChunk::_go /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469 STACK: Process::MpiChunk::run /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=snorf ERROR: Failed while gathering ab-init output files ERROR: Chunk failed at level:1, tier_type:2 FAILED CONTIG:chr1 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:chr1 examining contents of the fasta file and run log From preethibagopi5 at yahoo.com Wed Jun 12 04:40:11 2019 From: preethibagopi5 at yahoo.com (Preethiba Gopi) Date: Wed, 12 Jun 2019 15:10:11 +0530 Subject: [maker-devel] SNAP error in MAKER exon: out_of_bounds Message-ID: Hi, I am running a genome annotation in MAKER2 in which I completed the evidence round of maker and got a GFF3 file as output. I used the GFF3 file from the first maker run to train the SNAP in which it is showing me the error as this. All the gene models are showing errors. I checked with NCBI provided GFF3 file also to train SNAP but I ended up in same error telling that all gene models as error. **********Command Used***************** > maker2zff genome.all.gff > fathom -validate geneome.ann genome.dna > snap_validate.output.txt Can anyone please help me to solve this problem... Thanks in advance.? Sent from Mail for Windows 10 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 5993C86B977A41498422F781B46D3F46.png Type: image/png Size: 311209 bytes Desc: not available URL: From preethiba at 3bigs.com Wed Jun 12 04:42:58 2019 From: preethiba at 3bigs.com (PREETHIBA GOPI) Date: Wed, 12 Jun 2019 15:12:58 +0530 Subject: [maker-devel] SNAP error in MAKER exon:out_of_bounds Message-ID: Hi, I am running a genome annotation in MAKER2 in which I completed the evidence round of maker and got a GFF3 file as output. I used the GFF3 file from the first maker run to train the SNAP in which it is showing me the error as this. All the gene models are showing errors. I checked with NCBI provided GFF3 file also to train SNAP but I ended up in same error telling that all gene models as error. **********Command Used***************** > maker2zff genome.all.gff > fathom -validate geneome.ann genome.dna > snap_validate.output.txt Can anyone please help me to solve this problem... Thanks in advance. In addition to that I can't able to post the query in maker-devel google group [image: image.png] Please let me know what to do... -- Thanks and Regards, Preethiba G -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 54379 bytes Desc: not available URL: From carsonhh at gmail.com Tue Jun 25 16:07:59 2019 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Jun 2019 15:07:59 -0600 Subject: [maker-devel] Problems with ipr_update_gff In-Reply-To: References: Message-ID: <63352494-FFCB-4725-9344-307FB91F7DB7@gmail.com> It means the ID in the interproscan report and the GFF3 file are different This means either you have altered the names at some point so one does not match the other, or you ran interproscan on entries that are not gene models in the GFF3. For example you ran on the Snap or Augustus fast file rather than the maker proteins file. Since not all Snap/Augustus models are genes (it?s a raw report that includes rejected models) you have no corresponding gene/mRNA/exon/CDS feature in the GFF3 file to match with. ?Carson > On May 31, 2019, at 1:26 PM, Eduardo Conrado Souza Queiroz Nascimento wrote: > > Hi, I'm a graduate student at the Federal University of Rio de Janeiro in Brazil, I've been running into problems while trying to run the "ipr_update_gff" script. This message keeps showing and I haven't found a way to solve it. > > > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178309. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178310. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178310. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178312. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178312. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178313. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178313. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178314. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178314. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178315. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178315. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178316. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178316. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178317. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178317. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178318. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178318. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178319. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178319. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178320. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178320. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178320. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178321. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178321. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178321. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178322. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178322. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178324. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178324. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178325. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178325. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178326. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178326. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178327. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178327. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178328. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178328. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178329. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178329. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178330. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178330. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178331. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178331. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178331. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178332. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178332. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178333. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178333. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178335. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178335. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178336. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178336. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178337. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178337. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178338. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178338. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178339. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178339. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178340. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178340. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178341. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178341. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178342. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178342. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178343. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178343. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178344. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178344. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178345. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178345. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178345. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178346. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178346. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178346. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178347. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178347. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178349. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178349. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178350. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178350. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178351. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178351. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178351. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178352. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178352. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178353. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178353. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178353. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178353. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178354. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178354. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178355. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178355. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178356. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178356. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178357. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178357. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178358. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178358. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178359. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178359. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178360. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178360. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178361. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178361. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178362. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178362. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178363. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178363. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178364. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178364. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178365. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178365. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178367. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178367. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178368. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178368. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178369. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178369. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178369. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178370. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178370. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178371. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178371. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178371. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178372. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178372. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178372. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178373. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178373. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178374. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178374. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178375. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178375. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178376. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178376. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178377. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178377. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178379. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178379. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178380. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178380. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178381. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178381. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178382. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178382. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178383. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178383. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178383. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178384. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178384. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178385. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178385. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178386. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178386. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178387. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178387. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178388. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178388. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178389. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178389. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178389. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178389. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178390. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178390. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178390. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178391. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178391. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178392. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178392. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178393. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178393. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178393. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178393. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178394. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178394. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178395. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178395. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178395. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178395. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178396. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178396. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178397. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178397. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178398. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178398. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178399. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178399. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178400. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178400. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178401. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178401. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178402. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178402. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178402. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178402. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178403. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178403. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178404. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178404. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178405. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178405. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178406. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178406. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178407. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178407. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178408. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178408. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178409. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178409. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178410. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178410. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178411. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178411. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178412. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178412. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178413. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178413. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178414. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178414. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178415. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178415. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178416. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178416. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178417. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178417. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178418. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178418. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178419. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178419. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178420. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178420. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178420. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178420. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178421. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178421. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178422. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178422. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178422. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178422. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178423. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178423. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178424. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178424. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178425. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178425. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178426. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178426. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178427. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178427. > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From yuna.seagullbande at gmail.com Tue Jun 25 08:54:26 2019 From: yuna.seagullbande at gmail.com (Yuna) Date: Tue, 25 Jun 2019 15:54:26 +0200 Subject: [maker-devel] Maker train SNAP: substr outside of string at Carp.pm Message-ID: <310eb719-293f-8c51-dd38-f2361d184a28@gmail.com> Hi, I ran MAKER successfully to generate data for training SNAP. However, now I want to run the training round with MAKER (run MAKER with the hmm file), but MAKER fails for every contig it processed till now. The "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the gff header line) and the error massage is attached below. I can not figure out what the problem is. I? appreciate any help. Thank you! Log: gathering ab-init output files deleted:0 genes substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line 346. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Calling translate without a seq argument! STACK: Error::throw STACK: Bio::Root::Root::throw /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447 STACK: Bio::Tools::CodonTable::translate /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419 STACK: CGL::TranslationMachine::longest_translation_plus_stop /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280 STACK: maker::auto_annotator::get_translation_seq /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236 STACK: Widget::snap::load_phat_hits /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974 STACK: Widget::snap::parse /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690 STACK: GI::parse_abinit_file /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194 STACK: Process::MpiChunk::_go /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469 STACK: Process::MpiChunk::run /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=snorf ERROR: Failed while gathering ab-init output files ERROR: Chunk failed at level:1, tier_type:2 FAILED CONTIG:chr1 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:chr1 examining contents of the fasta file and run log From carsonhh at gmail.com Tue Jun 25 16:17:05 2019 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Jun 2019 15:17:05 -0600 Subject: [maker-devel] Maker train SNAP: substr outside of string at Carp.pm In-Reply-To: <310eb719-293f-8c51-dd38-f2361d184a28@gmail.com> References: <310eb719-293f-8c51-dd38-f2361d184a28@gmail.com> Message-ID: <09A54944-9A39-42D1-A50B-C278AFB6DB54@gmail.com> It dies trying to read SNAP?s result file. Check earlier in the log to see if there are any other errors. If not, run maker without MPI on a single CPU. You should be able to copy the command MAKER is using to call SNAP right before the failure. You can try running it outside of MAKER. My guess is there is a problem with SNAP failing and leaving a truncated report, or something in wrong with the training file SNAP is using. ?Carson > On Jun 25, 2019, at 7:54 AM, Yuna wrote: > > Hi, > > I ran MAKER successfully to generate data for training SNAP. However, now I want to run the training round with MAKER (run MAKER with the hmm file), but MAKER fails for every contig it processed till now. The "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the gff header line) and the error massage is attached below. I can not figure out what the problem is. > > I appreciate any help. Thank you! > > Log: > gathering ab-init output files > > deleted:0 genes > substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line 346. > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Calling translate without a seq argument! > STACK: Error::throw > STACK: Bio::Root::Root::throw /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447 > STACK: Bio::Tools::CodonTable::translate /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419 > STACK: CGL::TranslationMachine::longest_translation_plus_stop /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280 > STACK: maker::auto_annotator::get_translation_seq /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236 > STACK: Widget::snap::load_phat_hits /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974 > STACK: Widget::snap::parse /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690 > STACK: GI::parse_abinit_file /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194 > STACK: Process::MpiChunk::_go /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469 > STACK: Process::MpiChunk::run /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341 > STACK: Process::MpiChunk::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357 > STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 > STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 > STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686 > ----------------------------------------------------------- > --> rank=NA, hostname=snorf > ERROR: Failed while gathering ab-init output files > ERROR: Chunk failed at level:1, tier_type:2 > FAILED CONTIG:chr1 > > ERROR: Chunk failed at level:4, tier_type:0 > FAILED CONTIG:chr1 > > examining contents of the fasta file and run log > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From xvazquezc at gmail.com Tue Jun 25 18:42:55 2019 From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=) Date: Wed, 26 Jun 2019 09:42:55 +1000 Subject: [maker-devel] Maker train SNAP: substr outside of string at Carp.pm In-Reply-To: <09A54944-9A39-42D1-A50B-C278AFB6DB54@gmail.com> References: <310eb719-293f-8c51-dd38-f2361d184a28@gmail.com> <09A54944-9A39-42D1-A50B-C278AFB6DB54@gmail.com> Message-ID: Hi Yuna, adding to Carson's answer, check the output of maker2zff. If you don't have RNAseq data or any other high-quality evidences for annotation, chances are that the default parameters of maker2zff are too strict and are producing empty output files. Check the maker2zff --help and adjust the options as needed. In "worst case scenario" you may need to run it with "-n", which has no filtering at all in regards about which genes from the gff file to select. Cheers, Xabi On Wed, 26 Jun 2019 at 07:17, Carson Holt wrote: > It dies trying to read SNAP?s result file. Check earlier in the log to see > if there are any other errors. If not, run maker without MPI on a single > CPU. You should be able to copy the command MAKER is using to call SNAP > right before the failure. You can try running it outside of MAKER. My guess > is there is a problem with SNAP failing and leaving a truncated report, or > something in wrong with the training file SNAP is using. > > ?Carson > > > > On Jun 25, 2019, at 7:54 AM, Yuna wrote: > > > > Hi, > > > > I ran MAKER successfully to generate data for training SNAP. However, > now I want to run the training round with MAKER (run MAKER with the hmm > file), but MAKER fails for every contig it processed till now. The > "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the > gff header line) and the error massage is attached below. I can not figure > out what the problem is. > > > > I appreciate any help. Thank you! > > > > Log: > > gathering ab-init output files > > > > deleted:0 genes > > substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line > 346. > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Calling translate without a seq argument! > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447 > > STACK: Bio::Tools::CodonTable::translate > /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419 > > STACK: CGL::TranslationMachine::longest_translation_plus_stop > /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280 > > STACK: maker::auto_annotator::get_translation_seq > /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236 > > STACK: Widget::snap::load_phat_hits > /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974 > > STACK: Widget::snap::parse > /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690 > > STACK: GI::parse_abinit_file > /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194 > > STACK: Process::MpiChunk::_go > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469 > > STACK: Process::MpiChunk::run > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341 > > STACK: Process::MpiChunk::run_all > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357 > > STACK: Process::MpiTiers::run_all > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 > > STACK: Process::MpiTiers::run_all > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 > > STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686 > > ----------------------------------------------------------- > > --> rank=NA, hostname=snorf > > ERROR: Failed while gathering ab-init output files > > ERROR: Chunk failed at level:1, tier_type:2 > > FAILED CONTIG:chr1 > > > > ERROR: Chunk failed at level:4, tier_type:0 > > FAILED CONTIG:chr1 > > > > examining contents of the fasta file and run log > > > > > > _______________________________________________ > > maker-devel mailing list > > maker-devel at box290.bluehost.com > > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Xabier V?zquez-Campos, *PhD* *Research Associate* NSW Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 AUSTRALIA -------------- next part -------------- An HTML attachment was scrubbed... URL: From frommer at cebitec.uni-bielefeld.de Fri Jun 21 07:57:30 2019 From: frommer at cebitec.uni-bielefeld.de (Bianca Frommer) Date: Fri, 21 Jun 2019 15:57:30 +0200 Subject: [maker-devel] substr outside of string at Carp.pm Message-ID: <4d5aded5-7458-39a8-2507-34ab34d6ce42@cebitec.uni-bielefeld.de> Dear support team, I ran MAKER successfully to generate data for training SNAP. However, now I want to run the training round with MAKER (run MAKER with the hmm file), but MAKER fails for every contig it processed till now. The "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the gff header line) and the error massage is attached below. I can not figure out what the problem is. Thank you! Sincerely, Bianca gathering ab-init output files deleted:0 genes substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line 346. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Calling translate without a seq argument! STACK: Error::throw STACK: Bio::Root::Root::throw /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447 STACK: Bio::Tools::CodonTable::translate /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419 STACK: CGL::TranslationMachine::longest_translation_plus_stop /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280 STACK: maker::auto_annotator::get_translation_seq /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236 STACK: Widget::snap::load_phat_hits /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974 STACK: Widget::snap::parse /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690 STACK: GI::parse_abinit_file /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194 STACK: Process::MpiChunk::_go /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469 STACK: Process::MpiChunk::run /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=snorf ERROR: Failed while gathering ab-init output files ERROR: Chunk failed at level:1, tier_type:2 FAILED CONTIG:chr1 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:chr1 examining contents of the fasta file and run log From preethibagopi5 at yahoo.com Wed Jun 12 03:40:11 2019 From: preethibagopi5 at yahoo.com (Preethiba Gopi) Date: Wed, 12 Jun 2019 15:10:11 +0530 Subject: [maker-devel] SNAP error in MAKER exon: out_of_bounds Message-ID: Hi, I am running a genome annotation in MAKER2 in which I completed the evidence round of maker and got a GFF3 file as output. I used the GFF3 file from the first maker run to train the SNAP in which it is showing me the error as this. All the gene models are showing errors. I checked with NCBI provided GFF3 file also to train SNAP but I ended up in same error telling that all gene models as error. **********Command Used***************** > maker2zff genome.all.gff > fathom -validate geneome.ann genome.dna > snap_validate.output.txt Can anyone please help me to solve this problem... Thanks in advance.? Sent from Mail for Windows 10 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 5993C86B977A41498422F781B46D3F46.png Type: image/png Size: 311209 bytes Desc: not available URL: From preethiba at 3bigs.com Wed Jun 12 03:42:58 2019 From: preethiba at 3bigs.com (PREETHIBA GOPI) Date: Wed, 12 Jun 2019 15:12:58 +0530 Subject: [maker-devel] SNAP error in MAKER exon:out_of_bounds Message-ID: Hi, I am running a genome annotation in MAKER2 in which I completed the evidence round of maker and got a GFF3 file as output. I used the GFF3 file from the first maker run to train the SNAP in which it is showing me the error as this. All the gene models are showing errors. I checked with NCBI provided GFF3 file also to train SNAP but I ended up in same error telling that all gene models as error. **********Command Used***************** > maker2zff genome.all.gff > fathom -validate geneome.ann genome.dna > snap_validate.output.txt Can anyone please help me to solve this problem... Thanks in advance. In addition to that I can't able to post the query in maker-devel google group [image: image.png] Please let me know what to do... -- Thanks and Regards, Preethiba G -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 54379 bytes Desc: not available URL: From carsonhh at gmail.com Tue Jun 25 15:07:59 2019 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Jun 2019 15:07:59 -0600 Subject: [maker-devel] Problems with ipr_update_gff In-Reply-To: References: Message-ID: <63352494-FFCB-4725-9344-307FB91F7DB7@gmail.com> It means the ID in the interproscan report and the GFF3 file are different This means either you have altered the names at some point so one does not match the other, or you ran interproscan on entries that are not gene models in the GFF3. For example you ran on the Snap or Augustus fast file rather than the maker proteins file. Since not all Snap/Augustus models are genes (it?s a raw report that includes rejected models) you have no corresponding gene/mRNA/exon/CDS feature in the GFF3 file to match with. ?Carson > On May 31, 2019, at 1:26 PM, Eduardo Conrado Souza Queiroz Nascimento wrote: > > Hi, I'm a graduate student at the Federal University of Rio de Janeiro in Brazil, I've been running into problems while trying to run the "ipr_update_gff" script. This message keeps showing and I haven't found a way to solve it. > > > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178309. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178310. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178310. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178312. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178312. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178313. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178313. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178314. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178314. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178315. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178315. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178316. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178316. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178317. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178317. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178318. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178318. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178319. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178319. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178320. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178320. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178320. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178321. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178321. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178321. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178322. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178322. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178324. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178324. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178325. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178325. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178326. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178326. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178327. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178327. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178328. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178328. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178329. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178329. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178330. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178330. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178331. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178331. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178331. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178332. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178332. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178333. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178333. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178335. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178335. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178336. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178336. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178337. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178337. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178338. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178338. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178339. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178339. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178340. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178340. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178341. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178341. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178342. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178342. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178343. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178343. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178344. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178344. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178345. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178345. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178345. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178346. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178346. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178346. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178347. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178347. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178349. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178349. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178350. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178350. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178351. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178351. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178351. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178352. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178352. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178353. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178353. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178353. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178353. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178354. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178354. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178355. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178355. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178356. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178356. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178357. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178357. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178358. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178358. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178359. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178359. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178360. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178360. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178361. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178361. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178362. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178362. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178363. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178363. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178364. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178364. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178365. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178365. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178367. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178367. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178368. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178368. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178369. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178369. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178369. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178370. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178370. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178371. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178371. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178371. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178372. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178372. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178372. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178373. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178373. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178374. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178374. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178375. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178375. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178376. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178376. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178377. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178377. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178379. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178379. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178380. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178380. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178381. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178381. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178382. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178382. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178383. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178383. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178383. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178384. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178384. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178385. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178385. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178386. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178386. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178387. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178387. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178388. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178388. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178389. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178389. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178389. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178389. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178390. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178390. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178390. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178391. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178391. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178392. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178392. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178393. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178393. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178393. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178393. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178394. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178394. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178395. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178395. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178395. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178395. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178396. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178396. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178397. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178397. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178398. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178398. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178399. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178399. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178400. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178400. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178401. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178401. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178402. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178402. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178402. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178402. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178403. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178403. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178404. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178404. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178405. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178405. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178406. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178406. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178407. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178407. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178408. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178408. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178409. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178409. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178410. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178410. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178411. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178411. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178412. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178412. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178413. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178413. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178414. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178414. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178415. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178415. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178416. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178416. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178417. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178417. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178418. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178418. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178419. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178419. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178420. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178420. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178420. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178420. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178421. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178421. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178422. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178422. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178422. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178422. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178423. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178423. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178424. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178424. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178425. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178425. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178426. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178426. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178427. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178427. > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From yuna.seagullbande at gmail.com Tue Jun 25 07:54:26 2019 From: yuna.seagullbande at gmail.com (Yuna) Date: Tue, 25 Jun 2019 15:54:26 +0200 Subject: [maker-devel] Maker train SNAP: substr outside of string at Carp.pm Message-ID: <310eb719-293f-8c51-dd38-f2361d184a28@gmail.com> Hi, I ran MAKER successfully to generate data for training SNAP. However, now I want to run the training round with MAKER (run MAKER with the hmm file), but MAKER fails for every contig it processed till now. The "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the gff header line) and the error massage is attached below. I can not figure out what the problem is. I? appreciate any help. Thank you! Log: gathering ab-init output files deleted:0 genes substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line 346. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Calling translate without a seq argument! STACK: Error::throw STACK: Bio::Root::Root::throw /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447 STACK: Bio::Tools::CodonTable::translate /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419 STACK: CGL::TranslationMachine::longest_translation_plus_stop /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280 STACK: maker::auto_annotator::get_translation_seq /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236 STACK: Widget::snap::load_phat_hits /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974 STACK: Widget::snap::parse /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690 STACK: GI::parse_abinit_file /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194 STACK: Process::MpiChunk::_go /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469 STACK: Process::MpiChunk::run /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=snorf ERROR: Failed while gathering ab-init output files ERROR: Chunk failed at level:1, tier_type:2 FAILED CONTIG:chr1 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:chr1 examining contents of the fasta file and run log From carsonhh at gmail.com Tue Jun 25 15:17:05 2019 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Jun 2019 15:17:05 -0600 Subject: [maker-devel] Maker train SNAP: substr outside of string at Carp.pm In-Reply-To: <310eb719-293f-8c51-dd38-f2361d184a28@gmail.com> References: <310eb719-293f-8c51-dd38-f2361d184a28@gmail.com> Message-ID: <09A54944-9A39-42D1-A50B-C278AFB6DB54@gmail.com> It dies trying to read SNAP?s result file. Check earlier in the log to see if there are any other errors. If not, run maker without MPI on a single CPU. You should be able to copy the command MAKER is using to call SNAP right before the failure. You can try running it outside of MAKER. My guess is there is a problem with SNAP failing and leaving a truncated report, or something in wrong with the training file SNAP is using. ?Carson > On Jun 25, 2019, at 7:54 AM, Yuna wrote: > > Hi, > > I ran MAKER successfully to generate data for training SNAP. However, now I want to run the training round with MAKER (run MAKER with the hmm file), but MAKER fails for every contig it processed till now. The "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the gff header line) and the error massage is attached below. I can not figure out what the problem is. > > I appreciate any help. Thank you! > > Log: > gathering ab-init output files > > deleted:0 genes > substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line 346. > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Calling translate without a seq argument! > STACK: Error::throw > STACK: Bio::Root::Root::throw /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447 > STACK: Bio::Tools::CodonTable::translate /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419 > STACK: CGL::TranslationMachine::longest_translation_plus_stop /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280 > STACK: maker::auto_annotator::get_translation_seq /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236 > STACK: Widget::snap::load_phat_hits /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974 > STACK: Widget::snap::parse /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690 > STACK: GI::parse_abinit_file /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194 > STACK: Process::MpiChunk::_go /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469 > STACK: Process::MpiChunk::run /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341 > STACK: Process::MpiChunk::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357 > STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 > STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 > STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686 > ----------------------------------------------------------- > --> rank=NA, hostname=snorf > ERROR: Failed while gathering ab-init output files > ERROR: Chunk failed at level:1, tier_type:2 > FAILED CONTIG:chr1 > > ERROR: Chunk failed at level:4, tier_type:0 > FAILED CONTIG:chr1 > > examining contents of the fasta file and run log > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From xvazquezc at gmail.com Tue Jun 25 17:42:55 2019 From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=) Date: Wed, 26 Jun 2019 09:42:55 +1000 Subject: [maker-devel] Maker train SNAP: substr outside of string at Carp.pm In-Reply-To: <09A54944-9A39-42D1-A50B-C278AFB6DB54@gmail.com> References: <310eb719-293f-8c51-dd38-f2361d184a28@gmail.com> <09A54944-9A39-42D1-A50B-C278AFB6DB54@gmail.com> Message-ID: Hi Yuna, adding to Carson's answer, check the output of maker2zff. If you don't have RNAseq data or any other high-quality evidences for annotation, chances are that the default parameters of maker2zff are too strict and are producing empty output files. Check the maker2zff --help and adjust the options as needed. In "worst case scenario" you may need to run it with "-n", which has no filtering at all in regards about which genes from the gff file to select. Cheers, Xabi On Wed, 26 Jun 2019 at 07:17, Carson Holt wrote: > It dies trying to read SNAP?s result file. Check earlier in the log to see > if there are any other errors. If not, run maker without MPI on a single > CPU. You should be able to copy the command MAKER is using to call SNAP > right before the failure. You can try running it outside of MAKER. My guess > is there is a problem with SNAP failing and leaving a truncated report, or > something in wrong with the training file SNAP is using. > > ?Carson > > > > On Jun 25, 2019, at 7:54 AM, Yuna wrote: > > > > Hi, > > > > I ran MAKER successfully to generate data for training SNAP. However, > now I want to run the training round with MAKER (run MAKER with the hmm > file), but MAKER fails for every contig it processed till now. The > "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the > gff header line) and the error massage is attached below. I can not figure > out what the problem is. > > > > I appreciate any help. Thank you! > > > > Log: > > gathering ab-init output files > > > > deleted:0 genes > > substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line > 346. > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Calling translate without a seq argument! > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447 > > STACK: Bio::Tools::CodonTable::translate > /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419 > > STACK: CGL::TranslationMachine::longest_translation_plus_stop > /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280 > > STACK: maker::auto_annotator::get_translation_seq > /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236 > > STACK: Widget::snap::load_phat_hits > /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974 > > STACK: Widget::snap::parse > /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690 > > STACK: GI::parse_abinit_file > /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194 > > STACK: Process::MpiChunk::_go > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469 > > STACK: Process::MpiChunk::run > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341 > > STACK: Process::MpiChunk::run_all > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357 > > STACK: Process::MpiTiers::run_all > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 > > STACK: Process::MpiTiers::run_all > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 > > STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686 > > ----------------------------------------------------------- > > --> rank=NA, hostname=snorf > > ERROR: Failed while gathering ab-init output files > > ERROR: Chunk failed at level:1, tier_type:2 > > FAILED CONTIG:chr1 > > > > ERROR: Chunk failed at level:4, tier_type:0 > > FAILED CONTIG:chr1 > > > > examining contents of the fasta file and run log > > > > > > _______________________________________________ > > maker-devel mailing list > > maker-devel at box290.bluehost.com > > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Xabier V?zquez-Campos, *PhD* *Research Associate* NSW Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 AUSTRALIA -------------- next part -------------- An HTML attachment was scrubbed... URL: From frommer at cebitec.uni-bielefeld.de Fri Jun 21 07:57:30 2019 From: frommer at cebitec.uni-bielefeld.de (Bianca Frommer) Date: Fri, 21 Jun 2019 15:57:30 +0200 Subject: [maker-devel] substr outside of string at Carp.pm Message-ID: <4d5aded5-7458-39a8-2507-34ab34d6ce42@cebitec.uni-bielefeld.de> Dear support team, I ran MAKER successfully to generate data for training SNAP. However, now I want to run the training round with MAKER (run MAKER with the hmm file), but MAKER fails for every contig it processed till now. The "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the gff header line) and the error massage is attached below. I can not figure out what the problem is. Thank you! Sincerely, Bianca gathering ab-init output files deleted:0 genes substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line 346. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Calling translate without a seq argument! STACK: Error::throw STACK: Bio::Root::Root::throw /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447 STACK: Bio::Tools::CodonTable::translate /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419 STACK: CGL::TranslationMachine::longest_translation_plus_stop /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280 STACK: maker::auto_annotator::get_translation_seq /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236 STACK: Widget::snap::load_phat_hits /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974 STACK: Widget::snap::parse /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690 STACK: GI::parse_abinit_file /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194 STACK: Process::MpiChunk::_go /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469 STACK: Process::MpiChunk::run /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=snorf ERROR: Failed while gathering ab-init output files ERROR: Chunk failed at level:1, tier_type:2 FAILED CONTIG:chr1 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:chr1 examining contents of the fasta file and run log From preethibagopi5 at yahoo.com Wed Jun 12 03:40:11 2019 From: preethibagopi5 at yahoo.com (Preethiba Gopi) Date: Wed, 12 Jun 2019 15:10:11 +0530 Subject: [maker-devel] SNAP error in MAKER exon: out_of_bounds Message-ID: Hi, I am running a genome annotation in MAKER2 in which I completed the evidence round of maker and got a GFF3 file as output. I used the GFF3 file from the first maker run to train the SNAP in which it is showing me the error as this. All the gene models are showing errors. I checked with NCBI provided GFF3 file also to train SNAP but I ended up in same error telling that all gene models as error. **********Command Used***************** > maker2zff genome.all.gff > fathom -validate geneome.ann genome.dna > snap_validate.output.txt Can anyone please help me to solve this problem... Thanks in advance.? Sent from Mail for Windows 10 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 5993C86B977A41498422F781B46D3F46.png Type: image/png Size: 311209 bytes Desc: not available URL: From preethiba at 3bigs.com Wed Jun 12 03:42:58 2019 From: preethiba at 3bigs.com (PREETHIBA GOPI) Date: Wed, 12 Jun 2019 15:12:58 +0530 Subject: [maker-devel] SNAP error in MAKER exon:out_of_bounds Message-ID: Hi, I am running a genome annotation in MAKER2 in which I completed the evidence round of maker and got a GFF3 file as output. I used the GFF3 file from the first maker run to train the SNAP in which it is showing me the error as this. All the gene models are showing errors. I checked with NCBI provided GFF3 file also to train SNAP but I ended up in same error telling that all gene models as error. **********Command Used***************** > maker2zff genome.all.gff > fathom -validate geneome.ann genome.dna > snap_validate.output.txt Can anyone please help me to solve this problem... Thanks in advance. In addition to that I can't able to post the query in maker-devel google group [image: image.png] Please let me know what to do... -- Thanks and Regards, Preethiba G -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 54379 bytes Desc: not available URL: From carsonhh at gmail.com Tue Jun 25 15:07:59 2019 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Jun 2019 15:07:59 -0600 Subject: [maker-devel] Problems with ipr_update_gff In-Reply-To: References: Message-ID: <63352494-FFCB-4725-9344-307FB91F7DB7@gmail.com> It means the ID in the interproscan report and the GFF3 file are different This means either you have altered the names at some point so one does not match the other, or you ran interproscan on entries that are not gene models in the GFF3. For example you ran on the Snap or Augustus fast file rather than the maker proteins file. Since not all Snap/Augustus models are genes (it?s a raw report that includes rejected models) you have no corresponding gene/mRNA/exon/CDS feature in the GFF3 file to match with. ?Carson > On May 31, 2019, at 1:26 PM, Eduardo Conrado Souza Queiroz Nascimento wrote: > > Hi, I'm a graduate student at the Federal University of Rio de Janeiro in Brazil, I've been running into problems while trying to run the "ipr_update_gff" script. This message keeps showing and I haven't found a way to solve it. > > > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178309. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178310. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178310. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178312. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178312. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178313. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178313. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178314. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178314. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178315. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178315. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178316. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178316. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178317. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178317. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178318. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178318. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178319. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178319. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178320. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178320. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178320. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178321. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178321. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178321. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178322. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178322. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178324. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178324. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178325. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178325. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178326. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178326. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178327. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178327. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178328. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178328. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178329. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178329. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178330. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178330. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178331. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178331. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178331. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178332. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178332. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178333. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178333. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178335. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178335. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178336. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178336. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178337. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178337. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178338. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178338. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178339. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178339. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178340. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178340. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178341. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178341. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178342. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178342. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178343. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178343. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178344. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178344. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178345. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178345. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178345. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178346. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178346. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178346. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178347. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178347. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178349. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178349. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178350. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178350. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178351. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178351. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178351. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178352. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178352. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178353. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178353. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178353. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178353. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178354. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178354. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178355. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178355. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178356. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178356. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178357. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178357. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178358. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178358. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178359. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178359. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178360. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178360. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178361. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178361. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178362. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178362. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178363. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178363. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178364. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178364. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178365. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178365. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178367. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178367. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178368. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178368. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178369. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178369. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178369. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178370. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178370. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178371. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178371. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178371. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178372. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178372. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178372. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178373. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178373. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178374. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178374. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178375. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178375. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178376. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178376. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178377. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178377. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178379. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178379. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178380. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178380. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178381. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178381. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178382. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178382. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178383. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178383. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178383. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178384. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178384. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178385. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178385. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178386. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178386. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178387. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178387. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178388. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178388. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178389. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178389. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178389. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178389. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178390. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178390. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178390. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178391. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178391. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178392. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178392. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178393. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178393. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178393. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178393. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178394. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178394. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178395. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178395. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178395. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178395. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178396. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178396. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178397. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178397. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178398. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178398. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178399. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178399. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178400. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178400. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178401. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178401. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178402. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178402. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178402. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178402. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178403. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178403. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178404. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178404. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178405. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178405. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178406. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178406. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178407. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178407. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178408. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178408. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178409. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178409. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178410. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178410. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178411. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178411. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178412. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178412. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178413. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178413. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178414. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178414. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178415. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178415. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178416. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178416. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178417. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178417. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178418. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178418. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178419. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178419. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178420. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178420. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178420. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178420. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178421. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178421. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178422. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178422. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178422. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178422. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178423. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178423. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178424. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178424. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178425. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178425. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178426. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178426. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178427. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178427. > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From yuna.seagullbande at gmail.com Tue Jun 25 07:54:26 2019 From: yuna.seagullbande at gmail.com (Yuna) Date: Tue, 25 Jun 2019 15:54:26 +0200 Subject: [maker-devel] Maker train SNAP: substr outside of string at Carp.pm Message-ID: <310eb719-293f-8c51-dd38-f2361d184a28@gmail.com> Hi, I ran MAKER successfully to generate data for training SNAP. However, now I want to run the training round with MAKER (run MAKER with the hmm file), but MAKER fails for every contig it processed till now. The "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the gff header line) and the error massage is attached below. I can not figure out what the problem is. I? appreciate any help. Thank you! Log: gathering ab-init output files deleted:0 genes substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line 346. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Calling translate without a seq argument! STACK: Error::throw STACK: Bio::Root::Root::throw /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447 STACK: Bio::Tools::CodonTable::translate /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419 STACK: CGL::TranslationMachine::longest_translation_plus_stop /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280 STACK: maker::auto_annotator::get_translation_seq /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236 STACK: Widget::snap::load_phat_hits /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974 STACK: Widget::snap::parse /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690 STACK: GI::parse_abinit_file /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194 STACK: Process::MpiChunk::_go /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469 STACK: Process::MpiChunk::run /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=snorf ERROR: Failed while gathering ab-init output files ERROR: Chunk failed at level:1, tier_type:2 FAILED CONTIG:chr1 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:chr1 examining contents of the fasta file and run log From carsonhh at gmail.com Tue Jun 25 15:17:05 2019 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Jun 2019 15:17:05 -0600 Subject: [maker-devel] Maker train SNAP: substr outside of string at Carp.pm In-Reply-To: <310eb719-293f-8c51-dd38-f2361d184a28@gmail.com> References: <310eb719-293f-8c51-dd38-f2361d184a28@gmail.com> Message-ID: <09A54944-9A39-42D1-A50B-C278AFB6DB54@gmail.com> It dies trying to read SNAP?s result file. Check earlier in the log to see if there are any other errors. If not, run maker without MPI on a single CPU. You should be able to copy the command MAKER is using to call SNAP right before the failure. You can try running it outside of MAKER. My guess is there is a problem with SNAP failing and leaving a truncated report, or something in wrong with the training file SNAP is using. ?Carson > On Jun 25, 2019, at 7:54 AM, Yuna wrote: > > Hi, > > I ran MAKER successfully to generate data for training SNAP. However, now I want to run the training round with MAKER (run MAKER with the hmm file), but MAKER fails for every contig it processed till now. The "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the gff header line) and the error massage is attached below. I can not figure out what the problem is. > > I appreciate any help. Thank you! > > Log: > gathering ab-init output files > > deleted:0 genes > substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line 346. > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Calling translate without a seq argument! > STACK: Error::throw > STACK: Bio::Root::Root::throw /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447 > STACK: Bio::Tools::CodonTable::translate /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419 > STACK: CGL::TranslationMachine::longest_translation_plus_stop /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280 > STACK: maker::auto_annotator::get_translation_seq /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236 > STACK: Widget::snap::load_phat_hits /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974 > STACK: Widget::snap::parse /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690 > STACK: GI::parse_abinit_file /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194 > STACK: Process::MpiChunk::_go /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469 > STACK: Process::MpiChunk::run /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341 > STACK: Process::MpiChunk::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357 > STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 > STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 > STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686 > ----------------------------------------------------------- > --> rank=NA, hostname=snorf > ERROR: Failed while gathering ab-init output files > ERROR: Chunk failed at level:1, tier_type:2 > FAILED CONTIG:chr1 > > ERROR: Chunk failed at level:4, tier_type:0 > FAILED CONTIG:chr1 > > examining contents of the fasta file and run log > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From xvazquezc at gmail.com Tue Jun 25 17:42:55 2019 From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=) Date: Wed, 26 Jun 2019 09:42:55 +1000 Subject: [maker-devel] Maker train SNAP: substr outside of string at Carp.pm In-Reply-To: <09A54944-9A39-42D1-A50B-C278AFB6DB54@gmail.com> References: <310eb719-293f-8c51-dd38-f2361d184a28@gmail.com> <09A54944-9A39-42D1-A50B-C278AFB6DB54@gmail.com> Message-ID: Hi Yuna, adding to Carson's answer, check the output of maker2zff. If you don't have RNAseq data or any other high-quality evidences for annotation, chances are that the default parameters of maker2zff are too strict and are producing empty output files. Check the maker2zff --help and adjust the options as needed. In "worst case scenario" you may need to run it with "-n", which has no filtering at all in regards about which genes from the gff file to select. Cheers, Xabi On Wed, 26 Jun 2019 at 07:17, Carson Holt wrote: > It dies trying to read SNAP?s result file. Check earlier in the log to see > if there are any other errors. If not, run maker without MPI on a single > CPU. You should be able to copy the command MAKER is using to call SNAP > right before the failure. You can try running it outside of MAKER. My guess > is there is a problem with SNAP failing and leaving a truncated report, or > something in wrong with the training file SNAP is using. > > ?Carson > > > > On Jun 25, 2019, at 7:54 AM, Yuna wrote: > > > > Hi, > > > > I ran MAKER successfully to generate data for training SNAP. However, > now I want to run the training round with MAKER (run MAKER with the hmm > file), but MAKER fails for every contig it processed till now. The > "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the > gff header line) and the error massage is attached below. I can not figure > out what the problem is. > > > > I appreciate any help. Thank you! > > > > Log: > > gathering ab-init output files > > > > deleted:0 genes > > substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line > 346. > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Calling translate without a seq argument! > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447 > > STACK: Bio::Tools::CodonTable::translate > /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419 > > STACK: CGL::TranslationMachine::longest_translation_plus_stop > /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280 > > STACK: maker::auto_annotator::get_translation_seq > /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236 > > STACK: Widget::snap::load_phat_hits > /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974 > > STACK: Widget::snap::parse > /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690 > > STACK: GI::parse_abinit_file > /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194 > > STACK: Process::MpiChunk::_go > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469 > > STACK: Process::MpiChunk::run > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341 > > STACK: Process::MpiChunk::run_all > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357 > > STACK: Process::MpiTiers::run_all > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 > > STACK: Process::MpiTiers::run_all > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 > > STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686 > > ----------------------------------------------------------- > > --> rank=NA, hostname=snorf > > ERROR: Failed while gathering ab-init output files > > ERROR: Chunk failed at level:1, tier_type:2 > > FAILED CONTIG:chr1 > > > > ERROR: Chunk failed at level:4, tier_type:0 > > FAILED CONTIG:chr1 > > > > examining contents of the fasta file and run log > > > > > > _______________________________________________ > > maker-devel mailing list > > maker-devel at box290.bluehost.com > > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Xabier V?zquez-Campos, *PhD* *Research Associate* NSW Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 AUSTRALIA -------------- next part -------------- An HTML attachment was scrubbed... URL: From frommer at cebitec.uni-bielefeld.de Fri Jun 21 07:57:30 2019 From: frommer at cebitec.uni-bielefeld.de (Bianca Frommer) Date: Fri, 21 Jun 2019 15:57:30 +0200 Subject: [maker-devel] substr outside of string at Carp.pm Message-ID: <4d5aded5-7458-39a8-2507-34ab34d6ce42@cebitec.uni-bielefeld.de> Dear support team, I ran MAKER successfully to generate data for training SNAP. However, now I want to run the training round with MAKER (run MAKER with the hmm file), but MAKER fails for every contig it processed till now. The "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the gff header line) and the error massage is attached below. I can not figure out what the problem is. Thank you! Sincerely, Bianca gathering ab-init output files deleted:0 genes substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line 346. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Calling translate without a seq argument! STACK: Error::throw STACK: Bio::Root::Root::throw /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447 STACK: Bio::Tools::CodonTable::translate /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419 STACK: CGL::TranslationMachine::longest_translation_plus_stop /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280 STACK: maker::auto_annotator::get_translation_seq /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236 STACK: Widget::snap::load_phat_hits /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974 STACK: Widget::snap::parse /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690 STACK: GI::parse_abinit_file /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194 STACK: Process::MpiChunk::_go /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469 STACK: Process::MpiChunk::run /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=snorf ERROR: Failed while gathering ab-init output files ERROR: Chunk failed at level:1, tier_type:2 FAILED CONTIG:chr1 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:chr1 examining contents of the fasta file and run log From preethibagopi5 at yahoo.com Wed Jun 12 03:40:11 2019 From: preethibagopi5 at yahoo.com (Preethiba Gopi) Date: Wed, 12 Jun 2019 15:10:11 +0530 Subject: [maker-devel] SNAP error in MAKER exon: out_of_bounds Message-ID: Hi, I am running a genome annotation in MAKER2 in which I completed the evidence round of maker and got a GFF3 file as output. I used the GFF3 file from the first maker run to train the SNAP in which it is showing me the error as this. All the gene models are showing errors. I checked with NCBI provided GFF3 file also to train SNAP but I ended up in same error telling that all gene models as error. **********Command Used***************** > maker2zff genome.all.gff > fathom -validate geneome.ann genome.dna > snap_validate.output.txt Can anyone please help me to solve this problem... Thanks in advance.? Sent from Mail for Windows 10 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 5993C86B977A41498422F781B46D3F46.png Type: image/png Size: 311209 bytes Desc: not available URL: From preethiba at 3bigs.com Wed Jun 12 03:42:58 2019 From: preethiba at 3bigs.com (PREETHIBA GOPI) Date: Wed, 12 Jun 2019 15:12:58 +0530 Subject: [maker-devel] SNAP error in MAKER exon:out_of_bounds Message-ID: Hi, I am running a genome annotation in MAKER2 in which I completed the evidence round of maker and got a GFF3 file as output. I used the GFF3 file from the first maker run to train the SNAP in which it is showing me the error as this. All the gene models are showing errors. I checked with NCBI provided GFF3 file also to train SNAP but I ended up in same error telling that all gene models as error. **********Command Used***************** > maker2zff genome.all.gff > fathom -validate geneome.ann genome.dna > snap_validate.output.txt Can anyone please help me to solve this problem... Thanks in advance. In addition to that I can't able to post the query in maker-devel google group [image: image.png] Please let me know what to do... -- Thanks and Regards, Preethiba G -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 54379 bytes Desc: not available URL: From carsonhh at gmail.com Tue Jun 25 15:07:59 2019 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Jun 2019 15:07:59 -0600 Subject: [maker-devel] Problems with ipr_update_gff In-Reply-To: References: Message-ID: <63352494-FFCB-4725-9344-307FB91F7DB7@gmail.com> It means the ID in the interproscan report and the GFF3 file are different This means either you have altered the names at some point so one does not match the other, or you ran interproscan on entries that are not gene models in the GFF3. For example you ran on the Snap or Augustus fast file rather than the maker proteins file. Since not all Snap/Augustus models are genes (it?s a raw report that includes rejected models) you have no corresponding gene/mRNA/exon/CDS feature in the GFF3 file to match with. ?Carson > On May 31, 2019, at 1:26 PM, Eduardo Conrado Souza Queiroz Nascimento wrote: > > Hi, I'm a graduate student at the Federal University of Rio de Janeiro in Brazil, I've been running into problems while trying to run the "ipr_update_gff" script. This message keeps showing and I haven't found a way to solve it. > > > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178309. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178310. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178310. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178312. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178312. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178313. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178313. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178314. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178314. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178315. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178315. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178316. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178316. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178317. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178317. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178318. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178318. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178319. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178319. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178320. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178320. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178320. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178321. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178321. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178321. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178322. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178322. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178324. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178324. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178325. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178325. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178326. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178326. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178327. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178327. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178328. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178328. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178329. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178329. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178330. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178330. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178331. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178331. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178331. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178332. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178332. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178333. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178333. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178335. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178335. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178336. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178336. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178337. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178337. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178338. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178338. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178339. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178339. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178340. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178340. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178341. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178341. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178342. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178342. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178343. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178343. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178344. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178344. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178345. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178345. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178345. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178346. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178346. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178346. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178347. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178347. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178349. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178349. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178350. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178350. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178351. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178351. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178351. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178352. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178352. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178353. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178353. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178353. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178353. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178354. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178354. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178355. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178355. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178356. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178356. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178357. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178357. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178358. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178358. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178359. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178359. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178360. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178360. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178361. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178361. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178362. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178362. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178363. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178363. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178364. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178364. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178365. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178365. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178367. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178367. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178368. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178368. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178369. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178369. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178369. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178370. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178370. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178371. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178371. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178371. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178372. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178372. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178372. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178373. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178373. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178374. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178374. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178375. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178375. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178376. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178376. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178377. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178377. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178379. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178379. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178380. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178380. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178381. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178381. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178382. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178382. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178383. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178383. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178383. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178384. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178384. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178385. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178385. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178386. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178386. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178387. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178387. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178388. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178388. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178389. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178389. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178389. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178389. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178390. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178390. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178390. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178391. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178391. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178392. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178392. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178393. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178393. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178393. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178393. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178394. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178394. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178395. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178395. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178395. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178395. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178396. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178396. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178397. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178397. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178398. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178398. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178399. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178399. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178400. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178400. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178401. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178401. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178402. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178402. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178402. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178402. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178403. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178403. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178404. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178404. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178405. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178405. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178406. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178406. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178407. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178407. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178408. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178408. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178409. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178409. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178410. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178410. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178411. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178411. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178412. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178412. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178413. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178413. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178414. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178414. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178415. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178415. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178416. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178416. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178417. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178417. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178418. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178418. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178419. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178419. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178420. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178420. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178420. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178420. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178421. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178421. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178422. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178422. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178422. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178422. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178423. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178423. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178424. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178424. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178425. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178425. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178426. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178426. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178427. > Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178427. > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From yuna.seagullbande at gmail.com Tue Jun 25 07:54:26 2019 From: yuna.seagullbande at gmail.com (Yuna) Date: Tue, 25 Jun 2019 15:54:26 +0200 Subject: [maker-devel] Maker train SNAP: substr outside of string at Carp.pm Message-ID: <310eb719-293f-8c51-dd38-f2361d184a28@gmail.com> Hi, I ran MAKER successfully to generate data for training SNAP. However, now I want to run the training round with MAKER (run MAKER with the hmm file), but MAKER fails for every contig it processed till now. The "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the gff header line) and the error massage is attached below. I can not figure out what the problem is. I? appreciate any help. Thank you! Log: gathering ab-init output files deleted:0 genes substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line 346. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Calling translate without a seq argument! STACK: Error::throw STACK: Bio::Root::Root::throw /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447 STACK: Bio::Tools::CodonTable::translate /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419 STACK: CGL::TranslationMachine::longest_translation_plus_stop /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280 STACK: maker::auto_annotator::get_translation_seq /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236 STACK: Widget::snap::load_phat_hits /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974 STACK: Widget::snap::parse /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690 STACK: GI::parse_abinit_file /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194 STACK: Process::MpiChunk::_go /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469 STACK: Process::MpiChunk::run /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=snorf ERROR: Failed while gathering ab-init output files ERROR: Chunk failed at level:1, tier_type:2 FAILED CONTIG:chr1 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:chr1 examining contents of the fasta file and run log From carsonhh at gmail.com Tue Jun 25 15:17:05 2019 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 25 Jun 2019 15:17:05 -0600 Subject: [maker-devel] Maker train SNAP: substr outside of string at Carp.pm In-Reply-To: <310eb719-293f-8c51-dd38-f2361d184a28@gmail.com> References: <310eb719-293f-8c51-dd38-f2361d184a28@gmail.com> Message-ID: <09A54944-9A39-42D1-A50B-C278AFB6DB54@gmail.com> It dies trying to read SNAP?s result file. Check earlier in the log to see if there are any other errors. If not, run maker without MPI on a single CPU. You should be able to copy the command MAKER is using to call SNAP right before the failure. You can try running it outside of MAKER. My guess is there is a problem with SNAP failing and leaving a truncated report, or something in wrong with the training file SNAP is using. ?Carson > On Jun 25, 2019, at 7:54 AM, Yuna wrote: > > Hi, > > I ran MAKER successfully to generate data for training SNAP. However, now I want to run the training round with MAKER (run MAKER with the hmm file), but MAKER fails for every contig it processed till now. The "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the gff header line) and the error massage is attached below. I can not figure out what the problem is. > > I appreciate any help. Thank you! > > Log: > gathering ab-init output files > > deleted:0 genes > substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line 346. > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Calling translate without a seq argument! > STACK: Error::throw > STACK: Bio::Root::Root::throw /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447 > STACK: Bio::Tools::CodonTable::translate /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419 > STACK: CGL::TranslationMachine::longest_translation_plus_stop /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280 > STACK: maker::auto_annotator::get_translation_seq /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236 > STACK: Widget::snap::load_phat_hits /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974 > STACK: Widget::snap::parse /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690 > STACK: GI::parse_abinit_file /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194 > STACK: Process::MpiChunk::_go /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469 > STACK: Process::MpiChunk::run /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341 > STACK: Process::MpiChunk::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357 > STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 > STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 > STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686 > ----------------------------------------------------------- > --> rank=NA, hostname=snorf > ERROR: Failed while gathering ab-init output files > ERROR: Chunk failed at level:1, tier_type:2 > FAILED CONTIG:chr1 > > ERROR: Chunk failed at level:4, tier_type:0 > FAILED CONTIG:chr1 > > examining contents of the fasta file and run log > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From xvazquezc at gmail.com Tue Jun 25 17:42:55 2019 From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=) Date: Wed, 26 Jun 2019 09:42:55 +1000 Subject: [maker-devel] Maker train SNAP: substr outside of string at Carp.pm In-Reply-To: <09A54944-9A39-42D1-A50B-C278AFB6DB54@gmail.com> References: <310eb719-293f-8c51-dd38-f2361d184a28@gmail.com> <09A54944-9A39-42D1-A50B-C278AFB6DB54@gmail.com> Message-ID: Hi Yuna, adding to Carson's answer, check the output of maker2zff. If you don't have RNAseq data or any other high-quality evidences for annotation, chances are that the default parameters of maker2zff are too strict and are producing empty output files. Check the maker2zff --help and adjust the options as needed. In "worst case scenario" you may need to run it with "-n", which has no filtering at all in regards about which genes from the gff file to select. Cheers, Xabi On Wed, 26 Jun 2019 at 07:17, Carson Holt wrote: > It dies trying to read SNAP?s result file. Check earlier in the log to see > if there are any other errors. If not, run maker without MPI on a single > CPU. You should be able to copy the command MAKER is using to call SNAP > right before the failure. You can try running it outside of MAKER. My guess > is there is a problem with SNAP failing and leaving a truncated report, or > something in wrong with the training file SNAP is using. > > ?Carson > > > > On Jun 25, 2019, at 7:54 AM, Yuna wrote: > > > > Hi, > > > > I ran MAKER successfully to generate data for training SNAP. However, > now I want to run the training round with MAKER (run MAKER with the hmm > file), but MAKER fails for every contig it processed till now. The > "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the > gff header line) and the error massage is attached below. I can not figure > out what the problem is. > > > > I appreciate any help. Thank you! > > > > Log: > > gathering ab-init output files > > > > deleted:0 genes > > substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line > 346. > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Calling translate without a seq argument! > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447 > > STACK: Bio::Tools::CodonTable::translate > /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419 > > STACK: CGL::TranslationMachine::longest_translation_plus_stop > /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280 > > STACK: maker::auto_annotator::get_translation_seq > /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236 > > STACK: Widget::snap::load_phat_hits > /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974 > > STACK: Widget::snap::parse > /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690 > > STACK: GI::parse_abinit_file > /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194 > > STACK: Process::MpiChunk::_go > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469 > > STACK: Process::MpiChunk::run > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341 > > STACK: Process::MpiChunk::run_all > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357 > > STACK: Process::MpiTiers::run_all > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 > > STACK: Process::MpiTiers::run_all > /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287 > > STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686 > > ----------------------------------------------------------- > > --> rank=NA, hostname=snorf > > ERROR: Failed while gathering ab-init output files > > ERROR: Chunk failed at level:1, tier_type:2 > > FAILED CONTIG:chr1 > > > > ERROR: Chunk failed at level:4, tier_type:0 > > FAILED CONTIG:chr1 > > > > examining contents of the fasta file and run log > > > > > > _______________________________________________ > > maker-devel mailing list > > maker-devel at box290.bluehost.com > > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Xabier V?zquez-Campos, *PhD* *Research Associate* NSW Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 AUSTRALIA -------------- next part -------------- An HTML attachment was scrubbed... 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