search

williamritchie / IRFinder

Detecting intron retention from RNA-Seq experiments
53 stars 25 forks source link

Segmentation fault while aligning #60

Open ganguvamshi opened 5 years ago

ganguvamshi commented 5 years ago

Hi, I'm ending up segmentation fault while running the quantification step. Looks like some problem with alignment. I'm using ENSEMBL reference gtf and fasta files and the genome reference build was successful. Could you please help me resolving this issue?

Thanks!

Screenshot 2019-04-29 at 10 34 06 AM
dg520 commented 5 years ago

Hi @ganguvamshi ,

Looks like a C crash. Which version of GCC are you using? What OS is that? You might want to re-compile the IRFinder core from source at src/irfinder against your own system environment. And then replace the irfinder under bin/util with your newly compiled one. Please note, you need C++ 11 libraries and features to compile IRFinder, so a GCC version no less than than 4.9.0 is required. Try to re-run the alignment after completing the above steps and let me know. Thanks.

Best, Dadi