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wangjr03 / FLAMINGO

MIT License
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running issues with 7_reconstruct_within_cellline.R #17

Open poflawless opened 11 months ago

poflawless commented 11 months ago

Hello,

When I run the seventh step as you shown in the readme

for i in {1..50};do Rscript 7_reconstruct_within_cellline.R 0.5 10 0.3 ../chr21/GM12878/chr21_5kb_frag/Dist_frag${i}.txt ../chr21/GM12878/chr21_5kb_frag/IF_frag${i}.txt 5kb_frag${i} ../chr21/GM12878/result_0.5; done

I came up with

Error in checkForRemoteErrors(val): 2 nodes produced errors; first error: index out of range Calls: parLapply ... clusterApply -> staticClusterApply -> checkForRemoteErrors Execution stopped

Could you please tell me what is the possible solutions?

Best Wishes,

JiaxinYangJX commented 11 months ago

Thanks for using our software. The issues came from parallel computing. Please request enough CPUs to run the script. FYI, we set n_cores = 28 in Rscript 7_reconstruct_within_cellline.R by default, you can customize it based on the number of CPUs you requested.

Also, our R package, FLAMINGOr, is more easy to use. And we will release a more user-friendly version by next month. Thanks!

JiaxinYangJX commented 7 months ago

Hi @poflawless Thanks for using our tools! We just released a lite version of FLAMINGO, which is faster, more memory-efficient, and more user-friendly. We fixed the majority of bugs and hope the new version could help. Below is the link. https://github.com/JiaxinYangJX/FLAMINGOrLite