Hi. I am running GeneMark-ES for ab initio gene annotation of insect genomes.
After GeneMark-ES completed, I get the seemingly final output file named genemark.gtf, but the following standard output error is also generated.
(in cleanup) (in cleanup) at /path-to/lib/site_perl/5.26.2/Object/InsideOut.pm line 1953 during global destruction.
The actual standard output error is the repeat of the above.
The genemark.gtf is like this:
$ tail genemark.gtf
scaffold_209549 GeneMark.hmm CDS 241 306 . + 2 gene_id "188161_g"; transcript_id "188161_t"; cds_type "Internal"; count "4_7";
scaffold_209549 GeneMark.hmm intron 307 328 0 + 1 gene_id "188161_g"; transcript_id "188161_t"; count "4_6";
scaffold_209549 GeneMark.hmm exon 329 361 0 + . gene_id "188161_g"; transcript_id "188161_t";
scaffold_209549 GeneMark.hmm CDS 329 361 . + 2 gene_id "188161_g"; transcript_id "188161_t"; cds_type "Internal"; count "5_7";
scaffold_209549 GeneMark.hmm intron 362 395 0 + 1 gene_id "188161_g"; transcript_id "188161_t"; count "5_6";
scaffold_209549 GeneMark.hmm exon 396 428 0 + . gene_id "188161_g"; transcript_id "188161_t";
scaffold_209549 GeneMark.hmm CDS 396 428 . + 2 gene_id "188161_g"; transcript_id "188161_t"; cds_type "Internal"; count "6_7";
scaffold_209549 GeneMark.hmm intron 429 457 0 + 1 gene_id "188161_g"; transcript_id "188161_t"; count "6_6";
scaffold_209549 GeneMark.hmm exon 458 517 0 + . gene_id "188161_g"; transcript_id "188161_t";
scaffold_209549 GeneMark.hmm CDS 458 517 . + 2 gene_id "188161_g"; transcript_id "188161_t"; cds_type "Internal"; count "7_7";
The point which I think strange is that 3rd line in the output file above doesn't contain "mRNA" or "gene", unlike the standard gtf file.
gmes.log ends with:
/path-to/gmes_petap.pl : [Sun Jul 19 22:22:38 2020] mv genemark.gtf.tmp genemark.gtf
Is the output file I have got all right? Thank you very much in advance.
Best,
