Segmentation fault (core dumped)

[KimberlyAcevedo]

Hello,
I have converted my fasta file and paired end reads to make a GTF file using augustus. However, when I am trying to index the fasta file (the gtf file is needed) I recieve an error. This error is "no exon lines in the GTF file". For this reason I have been trying convert_ensembl on gtftk. I am now receiving an error similar to #187. I think my error message stems from the exons missing and am not sure of what I can do differently.

My code is:
gtftk convert_ensembl -i AP147_as_REF_augustus.gtf > AP147_as_REF_ensembl.gtf

My error message is:
/pygtftk/bin/gtftk:53: DeprecationWarning: Use shutil.which instead of find_executable
if not find_executable("bedtools"):
Segmentation fault (core dumped)

I have attached a screenshot of the GTF file as the GTF file was created from the publicly available fastq files from BioProject accession number PRJNA911610.

Is this something you are able to assist me with? Thank you in advance for your time!

[dputhier]

Hi,
This problem seems to be a little bit of scope. I think you should first try to understand why there are no 'exon' lines in your GTF file (maybe contact the Augustus developer). I really don't have sufficient information and knowledge about your system to help you with the upstream analyses that lead to this GTF. If you fix this, I may help you with processing the file in gtftk.
Best