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songw01 / MEGENA

Multiscale embedded gene co-expression network analysis
GNU General Public License v3.0
48 stars 16 forks source link

Hello I am recieving the following warning when I am running the parallelized version of ddMEGENA(). #9

Open ghost opened 3 years ago

ghost commented 3 years ago

`1: In mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, : scheduled cores 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 13, 16, 17, 19 did not deliver results, all values of the jobs will be affected

2: In mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, : scheduled cores 1, 2, 3, 6, 7, 9, 10, 11, 13, 14, 15, 19 did not deliver results, all values of the jobs will be affected

3: In mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, : scheduled cores 1, 2, 3, 4, 6, 7, 8, 9, 12, 16, 18, 20 did not deliver results, all values of the jobs will be affected

4: In mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, : scheduled cores 1, 2, 3, 4, 7, 9, 10, 12, 14, 18, 19, 20 did not deliver results, all values of the jobs will be affected

5: In mclapply(argsList, FUN, mc.preschedule = preschedule, mc.set.seed = set.seed, : scheduled cores 1, 2, 3, 4, 6, 7, 8, 9, 14, 15, 17, 19 did not deliver results, all values of the jobs will be affected`

I do not know why?

songw01 commented 3 years ago

Hm...this is weird. MEGENA itself does not use mclapply within it. This is ddMEGENA implementation. My understanding is that the output from ddcor is fed into MEGENA pipeline to sparsify. Do you have this output prior to ddMEGENA run?

ghost commented 3 years ago

Hello thank you so much for your reply. The file itself is too big to upload on github directly... I placed the data and the script i used here: https://github.com/ashaypatel/For-ddMEGENA-Analysis/tree/main/sample_data_folder. Please check it out!

If you have any questions please feel to ask! Also change paths to wherever you decide to download the data.

(updated the repository for design matrix issues)

Any tips and suggestions would be appreciated! Sorry for any inconvenience, Best, Ashay Patel