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YaqiangCao / cLoops

Accurate and flexible loops calling tool for 3D genomic data.
https://yaqiangcao.github.io/cLoops/
MIT License
109 stars 17 forks source link

missing output with only jd2 files #7

Closed kkkaiqiang closed 5 years ago

kkkaiqiang commented 5 years ago

I'm running cLoops with two bedpe files with the following commands:

2018-12-10 11:30:11,918 INFO Command line: cLoops -f /home/ykq/Data/BL-Hi-C/BL01/bl01.rmdup.bedpe,/home/ykq/Data/BL-Hi-C/BL02/bl02.rmdup.bedpe -o run2 -m 0 -eps 1000,2500,5000,7500,10000 -minPts 10,15,20 -p 10 -w True -j True -s False -c -hic True -cut 0 -plot True -max_cut False 2018-12-10 11:30:11,918 INFO mode:0 eps:[1000, 2500, 5000, 7500, 10000] minPts:[20, 15, 10] hic:True

And there were only .jd and _disCutoff.pdf files, no loops file.

i wonder how i can get the loops from these results, or should i rerun the data?

cLoops,log file attached. cLoops.log

YaqiangCao commented 5 years ago

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

kkkaiqiang commented 5 years ago

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?

YaqiangCao commented 5 years ago

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