Entering edit mode
3.4 years ago
hydra_questions
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30
Hi all, I'm trying to do a DGE analysis on a non-model organism that has a published Augustus gff file & accompanying fasta file. I keep getting this error:
terminate called after throwing an instance of 'std::out_of_range'
what(): vector::_M_range_check
/home/alice/tmp.sh: line 27: 31318 Aborted STAR --runMode genomeGenerate --genomeDir $genomeDir --sjdbGTFfile $GTF --genomeFastaFiles $REFERENCE --runThreadN 4
I believe that the gff and fasta may not be labelled the same. I have included a small sample of what the gff and fasta look like.
GFF:
# start gene scaffold1.g8
scaffold1 AUGUSTUS gene 71594 80958 0.07 - . ID=scaffold1.g8
scaffold1 AUGUSTUS transcript 71594 80958 0.07 - . ID=scaffold1.g8.t1;Parent=scaffold1.g8
scaffold1 AUGUSTUS transcription_end_site 71594 71594 . - . Parent=scaffold1.g8.t1
..
# coding sequence = [atggggaatcgtggaatggaagatttaatccctatcgtaaacaagttgcaagatgcatttgcacaaattggtatagagt
..
# cacgacctccacctgtaccaagtcgaccttag]
# protein sequence = [MGNRGMEDLIPIVNKLQDAFAQIGIESPIDLPQIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTRRPLVLQLSYANT
..
# ASSANKPSMPSRPVSVAVAPRPQLDNPSVPRRPAPTRPVPSQPPQPARPPPVPSRP]
FASTA:
scaffold1 len=5136627
TATACTACATATGATTTTTTATAGATAAAAAATCATATGTAGTatatttattgcaaaaaaaaactcacatataacatatttatttcaataaaaaactatt
gagtgatttttctgaaatcccccttccagaattgacagtggttttaaatgcatgtcttttactaccctaagctattcaaaaggaaatagcttacaaattt
..
Please let me know if you have any idea how to make the files similar, or any advice on how to make this work.
Thanks in advance!!