Hi
Attempted to run cuffmerge and received the following error:
You are using Cufflinks v2.0.0, which is the most recent release.
Error: duplicate GFF ID 'Cre01.g000050.t1.2' encountered!
[FAILED]
Error: could not execute cuffcompare
I checked the ref.gtf file for the record and it is unique:
less Au10.2E.201009combined_ch.gtf|grep Cre01.g000050.t1.2
chromosome_1 AUGUSTUS transcript 8846 14517 0.09 + . Cre01.g000050.t1.2;
chromosome_1 AUGUSTUS tss 8846 8846 . + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS 5'-UTR 8846 9014 0.39 + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS start_codon 9015 9017 . + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS initial 9015 12007 0.92 + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS internal 12193 12546 1 + 1 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS internal 12744 12993 1 + 1 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS terminal 13249 13479 1 + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS intron 12008 12192 1 + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS intron 12547 12743 1 + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS intron 12994 13248 1 + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS CDS 9015 12007 0.92 + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS CDS 12193 12546 1 + 1 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS CDS 12744 12993 1 + 1 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS CDS 13249 13479 1 + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS stop_codon 13477 13479 . + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS 3'-UTR 13480 14517 0.21 + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS tts 14517 14517 . + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
cuffmerge command was:
cuffmerge -g Au10.2E.201009combined_ch.gtf -s ~ref.fa assemblies.txt
Ideas?
Charles
Attempted to run cuffmerge and received the following error:
You are using Cufflinks v2.0.0, which is the most recent release.
Error: duplicate GFF ID 'Cre01.g000050.t1.2' encountered!
[FAILED]
Error: could not execute cuffcompare
I checked the ref.gtf file for the record and it is unique:
less Au10.2E.201009combined_ch.gtf|grep Cre01.g000050.t1.2
chromosome_1 AUGUSTUS transcript 8846 14517 0.09 + . Cre01.g000050.t1.2;
chromosome_1 AUGUSTUS tss 8846 8846 . + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS 5'-UTR 8846 9014 0.39 + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS start_codon 9015 9017 . + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS initial 9015 12007 0.92 + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS internal 12193 12546 1 + 1 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS internal 12744 12993 1 + 1 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS terminal 13249 13479 1 + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS intron 12008 12192 1 + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS intron 12547 12743 1 + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS intron 12994 13248 1 + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS CDS 9015 12007 0.92 + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS CDS 12193 12546 1 + 1 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS CDS 12744 12993 1 + 1 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS CDS 13249 13479 1 + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS stop_codon 13477 13479 . + 0 transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS 3'-UTR 13480 14517 0.21 + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
chromosome_1 AUGUSTUS tts 14517 14517 . + . transcript_id "Cre01.g000050.t1.2"; gene_id "Cre01.g000050";
cuffmerge command was:
cuffmerge -g Au10.2E.201009combined_ch.gtf -s ~ref.fa assemblies.txt
Ideas?
Charles
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