error at get_sigcell_simple() about scavenge HOT 7 CLOSED

Hi, following up to see if you guys had any suggestions to resolve this error. Thanks

from scavenge.

Hi, sorry for the late reply! I have no idea about this error, can you post more information about your data and output? Thank you!

from scavenge.

Hi, I used ~3000 fine-mapped SNPs as input and here is the RSE object with peak count matrix. TRS gets calculated successfully but not the permutation step. I see that there is a discrepancy in the no. of cells - 200071 is original rse but np_score was calculated only for 199779 cells. Could this be the issue? but seems unlikely becuase permutation step does not use original rse. please let me know if you would like to look at a specific output from the pipeline. Thank you!
class: RangedSummarizedExperiment
dim: 6 200071
metadata(0):
assays(1): counts
rownames: NULL
rowData names(2): bias idx
colnames(200071): atac_A1B1#CACCACTTCCAGGTAT-1
atac_A1B1#GTAGGAGTCCGGGCAT-1 ... atac_A28B28#TGCTATTAGAGTGGTC-1
atac_A28B28#CCTTGCATCGCAAGCC-1
colData names(123): orig.ident nCount_peaks ... nCount_RNA nFeature_RNA

from scavenge.

Thank you for the info.
I figure the discrepancy is not the cause of this error if your input for the dimension of knn_sparse_mat and length of topseed_npscore matched. I noticed that in your previous error there is a number of 199764 that should be the number related to the permutation output, which is different than the number of your input 199779. I think this could be the key. Can you post the entire error message of this analysis? thank you!

from scavenge.

1000
Stationary step: 80
Stationary Delta: 9.63450666772587e-06
Stationary step: 81
Stationary Delta: 9.48843841608067e-06
Stationary step: 74
Stationary Delta: 9.99591098634589e-06
Stationary step: 74
Stationary Delta: 9.44719369263237e-06
Stationary step: 74
Stationary Delta: 9.4838064933629e-06
Stationary step: 75
Stationary Delta: 9.79173786751816e-06
Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, :
arguments imply differing number of rows: 0, 199845
Calls: get_sigcell_simple ... as.data.frame -> as.data.frame.list -> do.call ->
In addition: Warning message:
In mclapply(1:permutation_times, mc.cores = mycores, function(i) { :
scheduled cores 1, 2, 3 did not deliver results, all values of the jobs will be affected
Execution halted
slurmstepd: error: Detected 3 oom-kill event(s) in StepId=1237064.batch. Some of your processes may have been killed by the cgroup out-of-memory handler.

from scavenge.

It seems that a out-of-memory issue, can you increase the memory of each core or use one core to process? Also, can you post how it goes with just 100 times permutation for 1 core and 4 cores, respectively?

from scavenge.

Hi, this was resolved with 5 cores and more memory!
Thanks

from scavenge.