#10 CIRI not progressing past second scan

[Lachlan G Gray]

Hi Yuan Gao,

I have been attempting to run CIRI in preparation for CIRI-AS on a HPC with increasing computational performance. Unforntunately, each time I run CIRI the program times out before the second scan begins.
The input files are paired-end human samples and the code (without pathnames) I am using is:

perl CIRI_v1.2.pl -P -I input.sam -O output.txt -F hg19.fa -A gencode.v19.annotation.gtf

Do you know why the program does not progress past second scanning?

Thank you kindly in advance,

Lachlan Gray

[Yuan Gao]

CIRI v1.2 needs more time and memory. Please use latest version v2.0.6 for your analysis. If the results will be further used for CIRI-AS, please make sure the read length is the same.