Re: MAKER finishes but I see some error msgs in stdout
Re: MAKER finishes but I see some error msgs in stdoutThe first error is likely caused by a formatting issue in your /data/lab_data/community.pine/AUGUSTUS/using-mskdSEQ/AGS_prd_gene_pita-GMap_usingMsked.gff3 file. If this was produced directly by Augustus, it is important to know that Augustus does not always produce correct GFF3 and often requires manual corrections.
The second error, is something I also noticed on a maize dataset I’ve been working with. It is caused by a partial gene model having a CDS longer than the exon (can happen if last codon is 2 base pairs long and because of third base pair ambiguity it can still translated). MAKER is supposed to fix these last codons in version 2, but was not in some specific scenarios.
Sorry for troubling you in the middle of holiday.
Having seen the successful run of particular trouble causing sequence, I started the maker run with the whole data. It is finished but I see some error messages in the nohup.out which I attach here(http://www.sendspace.com/file/jn6r46) along with the ctl files. Please let me know of this.