Open ks164 opened 1 week ago
ks164@duke.edu
03b-methylation_adjustment1.sh
adjustment of methylation data at step 03b fails for my family data (MZ and DZ twins).
I run the script in parallel, and each of the 100 batches are halted with one of the two following errors:
./03b-methylation_adjustment1.sh: line 78: 1987504 Killed ${R_directory}Rscript resources/methylation/adjust_pedigree.R ${home_directory} ${methylation_no_outliers} ${grmfile_relateds} ${covariates_combined}.txt ${transformed_methylation_adjusted} transformed ${nthreads} ${meth_chunks} ${i} ${methylation_array}
OR
Probe 1 of 91 Error in .rowNamesDF<-(x, value = value) : invalid 'row.names' length Calls: main ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<- Execution halted
.rowNamesDF<-
I did notice that the eigenvectors calculated seem to be zero:
Reading methylation data... Reading IDs Reading GRM Reading N Creating data frame Kinship matrix is 1502 by 1502 Calculating eigenvectors list List of 2 $ values : num [1:1502] 4.32 4.31 4.29 4.27 4.16 ... $ vectors: num [1:1502, 1:1502] 0 0 0 0 0 0 0 0 0 0 ... NULL
Attached are two example log files (the output is too big to paste)
log.txt1.txt log.txt100.txt
No response
4.3.3 (February, 2024)
None
Contact Details
ks164@duke.edu
Scripts
03b-methylation_adjustment1.sh
What happened?
adjustment of methylation data at step 03b fails for my family data (MZ and DZ twins).
I run the script in parallel, and each of the 100 batches are halted with one of the two following errors:
./03b-methylation_adjustment1.sh: line 78: 1987504 Killed ${R_directory}Rscript resources/methylation/adjust_pedigree.R ${home_directory} ${methylation_no_outliers} ${grmfile_relateds} ${covariates_combined}.txt ${transformed_methylation_adjusted} transformed ${nthreads} ${meth_chunks} ${i} ${methylation_array}
OR
Probe 1 of 91 Error in
.rowNamesDF<-(x, value = value) : invalid 'row.names' length Calls: main ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<- Execution haltedI did notice that the eigenvectors calculated seem to be zero:
Reading methylation data... Reading IDs Reading GRM Reading N Creating data frame Kinship matrix is 1502 by 1502 Calculating eigenvectors list List of 2 $ values : num [1:1502] 4.32 4.31 4.29 4.27 4.16 ... $ vectors: num [1:1502, 1:1502] 0 0 0 0 0 0 0 0 0 0 ... NULL
Attached are two example log files (the output is too big to paste)
log.txt1.txt log.txt100.txt
How can the bug be reproduced?
No response
R version
4.3.3 (February, 2024)
Python version
None
Relevant log output
No response