search

itmat / Normalization

RNA-Seq normalization and quantification pipeline
https://github.com/itmat/normalization/wiki
GNU General Public License v3.0
10 stars 5 forks source link

sam2cov #15

Closed jenruss closed 10 years ago

jenruss commented 10 years ago

I tried using sam2cov today for my human RNA-Seq data set. When I try to run it for my unique aligning reads, the program always stops and gives the following error message: "[ERROR](functions.c:226:make_entry_for_read errno: None) Could not find . /home/jenruss/RNA-SeqData/shell_scripts/C.05175_TDPpos.sam2cov.sh: line 1: 3656 Segmentation fault (core dumped) /home/jenruss/sam2cov/sam2cov -u -p /home/jenruss/RNA-SeqData/NORMALIZED_DATA/FINAL_SAM/Unique/05175_TDPpos.FINAL. /home/jenruss/hg19/hg19.fa.fai /home/jenruss/RNA-SeqData/NORMALIZED_DATA/FINAL_SAM/Unique/05175_TDPpos.FINAL.norm_u.sam". Can you please check what is the problem here and let me know?

khayer commented 10 years ago

This probably means the program ran out of memory. We will change the scripts accordingly.

eunjijunekim commented 10 years ago

runall_sam2cov.pl script has been updated.