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ay-lab / dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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Error in checkForRemoteErrors when performing PCA on cis interaction matrix #28

Closed QianzhaoJ closed 2 years ago

QianzhaoJ commented 2 years ago

Hi, Thanks for developing such powerful tools! But I got some errors when I performed PCA on cis interaction matrix. Command:Rscript /share/home/jiqianzhao/04_Softwares/dcHiC-master/dchicf.r --file dchic.sum.info.txt --pcatype cis --dirovwt T --cthread 2 --pthread 4 and Errors:Error in checkForRemoteErrors(val) : 2 nodes produced errors; first error: Two levels of parallelism are used. See?assert_cores.Calls: lapply ... clusterApply -> staticClusterApply -> checkForRemoteErrors When I tried Rscript /share/home/jiqianzhao/04_Softwares/dcHiC-master/dchicf.r --file dchic.sum.info.txt --pcatype cis --dirovwt T with default threads, it worked but run slowly. Could you give me some suggestions? Thanks in advance ! Best, Qianzhao

ay-lab commented 2 years ago

Hi! This doesn't seem to be a dcHiC-native issue; I think this error message is a check that comes from bigstatsr since too much parallelism can slow down computations: see this link and this one. I would recommend trying less parallel c/pthreads.

If the issue seems deeper than that or you think it may be dcHiC-related, feel free to give more information or shoot an email at jeffreywang@lji.org.