—Carson
On Apr 17, 2018, at 6:54 AM, Jacques Dainat <jacques...@nbis.se> wrote:I tried with the last version 3.01.02-beta, still the same error.I agree that it could be something wrong with the input GFF3 file, but I don’t find what it could be.I have loaded the whole folder as user guest_5602.I’m looking forward to hearing from you./JacquesOn 16 Apr 2018, at 22:11, Carson Holt <cars...@gmail.com> wrote:I can’t replicate your failure. Normally this error indicates there is something wrong with the input GFF3 file.If you want, you can run this on your own machine to generate the failure, then tarball up the complete maker directory for the failure and upload it here —> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgiAlso try the most current version of MAKER (3.01.02 - October 2017). See if it happens for you there.—CarsonOn Apr 13, 2018, at 6:52 AM, Jacques Dainat <jacques...@nbis.se> wrote:Dear Carson,<9529.1.136329.CGATGT.gff3>I come back to you still with the same problem: substr outside of string at /sw/bioinfo/maker/3.01.1-beta-OMPI/bin/../lib/PhatHit_utils.pm line 850.Since our last conversation in January I have seen in the MAKER mailing list that one more person (seoanezonjic) had this issue.In January, the only way I found to avoid the problem was to remove the gff files that were related to the issue.I have again the problem for a new annotation project. On the 6 `EST` gff files I’m using (produced in the same way, with Stringtie and converted in gff3 alignment style), 2 of them are raising the error.To try to better get where the problem come from I have minimise the tools used within MAKER. So no repeat masking and abinitio tools activated, only protein in fasta format and one EST file in gff format.Using only the gff est file with est2genome=1 worksUsing only protein in fasta with protein2genome worksUsing the gff EST file and the protein in fasta format with protein2genome and est2genome or only protein2genome doesn’t workThe problem occurs when protein alignments try to be extended by the EST information.I tried using the same tool versions as you (BioPerl 1.007002, BLAST+ 2.7.1, Exonerate 2.2.0) but still the same problem.One of the interesting thing is that the problem does not occur when I used the protein in gff format.Here is one gff file raising the error. If you want to try in the same conditions you will have to use/dowmload the swissprot database (uniprot rewieved only).<scaffold_1017.fa>I hope we will finish to find a solution to this problem…Best regards,Jacques-------------------------------------------------Jacques Dainat, Ph.D.NBIS (National Bioinformatics Infrastructure Sweden)Genome Annotation ServiceAddress:Uppsala University, Biomedicinska CentrumHusargatan 3, box 582
Department of Medical Biochemistry Microbiology, GenomicsS-75123 Uppsala SwedenPhone: +46 18 471 46 25