Hey all, I've been stalking this website for a few months for help (with success), and now I've run into my first problem that I can't solve :O . I am a wet-biologist by training so I'm still a noob at bioinformatics!
I am using STAR for E. coli reads and lately I have been receiving "segmentation Fault" error during the mapping portion. I have about 25 Gb of free RAM and read/write/execute permissions all set for user. I am using Debian and tried using both STAR versions2.5 & 2.6 I do not think anything is wrong with my code...
STAR --runThreadN 3 --genomeDir /home/jonathan7/Documents/Comp_Micro/STAR/Escherchia_coli_UTI89/ --sjdbGTFfile /home/jonathan7/Documents/Comp_Micro/STAR/Escherchia_coli_UTI89/UTI89_annotation.gtf --sjdbOverhang 100 --readFilesIn /home/jonathan7/Documents/Comp_Micro/STAR/Escherchia_coli_UTI89/UTI89_PostTrim1.fastq /home/jonathan7/Documents/Comp_Micro/STAR/Escherchia_coli_UTI89/UTI89_PostTrim2.fastq --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate Unsorted
Does anyone have a fix or some suggestions so I may continue troubleshooting?
Thanks for your time @Biostars, ~Jonathan J.S