missing output with only jd2 files about cloops HOT 3 CLOSED

Dear User,
According to the log, I can only judge that cLoops hasn't finished the running, so there is no result for .loop file.
I suggesting first using -c chr21 -cut 2000 to try see if cLoops can capture some significant loops.
Look forward to your feedback.
Best,
Yaqiang

from cloops.

Dear User,
According to the log, I can only judge that cLoops hasn't finished the running, so there is no result for .loop file.
I suggesting first using -c chr21 -cut 2000 to try see if cLoops can capture some significant loops.
Look forward to your feedback.
Best,
Yaqiang

Yaqiang,
Thanks a lot. I reran using -c chr21 -cut 2000 and it worked fine.
Is it possible that the input bedpe files were too big(20+G) so it crashed before finishing the p-values calculating? The input files are HiC data. Would specifying less eps parameters help?

from cloops.

Dear User,
According to the log, I can only judge that cLoops hasn't finished the running, so there is no result for .loop file.
I suggesting first using -c chr21 -cut 2000 to try see if cLoops can capture some significant loops.
Look forward to your feedback.
Best,
Yaqiang

Yaqiang,
Thanks a lot. I reran using -c chr21 -cut 2000 and it worked fine.
Is it possible that the input bedpe files were too big(20+G) so it crashed before finishing the p-values calculating? The input files are HiC data. Would specifying less eps parameters help?

Dear User,
What is the memory of you computer/server? If the memory are limited, then the crash could caused by the too big data.
However, from the estimated self-ligation vs. inter-ligation distance cutoff in the log file, I figure may be the data have a lot close PETs (such as within 10kb) ? I would suggest run -cut 2000 or 10000 for trial to get distant loops (also remove close PETs to save memory). Otherwise if you want close loops, then keep -cut small.
If you could give the chr21 data, I can adjust a parameter for you.
If you find cLoops nice for your data, please give us a star at github and cite it~
Best,
Yaqiang

from cloops.