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ay-lab / dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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error while running dcHiC #29

Closed Yuxinagli closed 2 years ago

Yuxinagli commented 2 years ago

Hi,

Thank you for the development of the dcHiC.

While I was using this tool to my Hi-C data, I stuck on the following error running "Rscript dchicf.r --file test_inputfiles.f.txt --pcatype cis --dirovwt T --cthread 2 --pthread 4". Could you please offer some help? ########################################### ... ... ... Calculating expected counts from chromosome wise background dist Weight 1 0 854838 2 100000 428198 3 200000 192287 4 300000 135688 5 400000 104093 6 500000 84077 A B Weight chr1 pos1 chr2 pos2 dist WeightOE 1: 23394 23394 640 chr9 0 chr9 0 0 0.9328551 2: 23394 23395 236 chr9 0 chr9 100000 100000 0.6861779 3: 23394 23396 117 chr9 0 chr9 200000 200000 0.7569310 4: 23394 23397 155 chr9 0 chr9 300000 300000 1.4199119 5: 23394 23398 76 chr9 0 chr9 400000 400000 0.9068045 6: 23394 23399 86 chr9 0 chr9 500000 500000 1.2693840 [1] 280317 [1] 17000000 [1] 280317 Writing chr9 .txt file Calculating expected counts from chromosome wise background Error in aggregate.data.frame(mf[1L], mf[-1L], FUN = FUN, ...) : no rows to aggregate Calls: lapply ... aggregate -> aggregate.formula -> aggregate.data.frame Execution halted rm: cannot remove '/home/xxx/xxx/tmp/RtmpVVQ6kO/sourceCpp-x86_64-pc-linux-gnu-1.0.7/sourcecpp_3bf462780119cc': Directory not empty

Thanks,

Yuxiang

ay-lab commented 2 years ago

Hi There—thank you for raising the issue. I'm not sure there's enough information to go from right here; did other chromosomes run this same part successfully before it failing on chromosome 9 (if so, it might be a data issue)?

Yuxinagli commented 2 years ago

Thank you very much for the reply! It works well after I deleted the 'chrM' and 'chrY' lines from the bed file according to the samples.

Thanks,

Yuxiang