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ay-lab / dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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error: Two levels of parallelism are used. See `?assert_cores`. #50

Closed Woohootakeoff closed 1 year ago

Woohootakeoff commented 1 year ago

error: Two levels of parallelism are used. See ?assert_cores.

Plz reply.Ths.

: Matrix dimension 1204 X 1204 Performing Z transformation : complete! Performing block wise correlation calculation : complete! Matrix dimension 6232 X 6232 Matrix dimension 880 X 880 Performing Z transformation : complete! Performing block wise correlation calculation : complete! Performing Z transformation : complete! Performing block wise correlation calculation : complete! Matrix dimension 5654 X 5654 Performing Z transformation : complete! Performing block wise correlation calculation : complete! Error in checkForRemoteErrors(val) : 2 nodes produced errors; first error: Two levels of parallelism are used. See ?assert_cores. Calls: lapply ... clusterApply -> staticClusterApply -> checkForRemoteErrors Execution halted

ay-lab commented 1 year ago

How many cores are you using? As an alternative option you can disable and run dcHiC with '--cthread 1 --pthread 1'

Woohootakeoff commented 1 year ago

thanks for your reply!Now i have a new error:(. please help again. in step 2: this is my command: Rscript dchicf.r --file dchic_code.txt --pcatype select --dirovwt T --genome hg19 and this is my dchic_code.txt : /E_40000_ym.matrix E_40000_abs_ym.bed E_40k exp1 K_40000_ym.matrix K_40000_abs_ym.bed K_40k exp2 and this is error: Running intra chr1 in E_40k sample Running intra chr2 in E_40k sample Error in hclust(as.dist(round(1 - cor(pc.mat), 4))) : NA/NaN/Inf in foreign function call (arg 10) Calls: pcselect -> pcselectioncore -> hclust Execution halted

as u see , it can run chr1,2 successfully ,then crash. and i can run STEP 1 " cis " successfully.

thanks for your help:))))))

ay-lab commented 1 year ago

Seems like it fails at the chr3 step. Can you check the chr3 PC values of E_40k, K_40k? The error may arise due to non-numerical values in the compartment score or noticed any anomalies in the compartment score (You can plot that too)?

Also to confirm that it is not due to a Hi-C resolution-specific issue, can you please run your dataset at 100Kb?

Woohootakeoff commented 1 year ago

Seems like it fails at the chr3 step. Can you check the chr3 PC values of E_40k, K_40k? The error may arise due to non-numerical values in the compartment score or noticed any anomalies in the compartment score (You can plot that too)?

Also to confirm that it is not due to a Hi-C resolution-specific issue, can you please run your dataset at 100Kb?

100kb is fine.Thank you very much.

ay-lab commented 1 year ago

Great! Happy to help you.