running issues with 7_reconstruct_within_cellline.R

[poflawless]

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]

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]

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