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,