Mem error while submitting job but works when ran with the R file

[Shrishtee-kandoi]

Script used:

Residual Expression: sQTL

sos run /restricted/projectnb/casa/xqtl-pipeline/pipeline/covariate_formatting.ipynb compute_residual \
        --cwd /restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/Covariate_data_preprocessing/ \
        --phenoFile /restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/leafcutter_output/batch_all_bam_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.gz \
        --covFile /restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/Covariate_data_preprocessing/ROSMAP_xqtl_covariates_sex_death_pmi_study.ROSMAP_NIA_WGS.leftnorm.filtered.related.filtered.extracted.pca.projected.gz \
        --container /restricted/projectnb/casa/xqtl-pipeline/container/singularity/bioinfo.sif \
        --walltime 100h \
        --numThreads 20 \
        --mem 100G -J 50 -c csg.yml -q neurology

Error:

INFO: Running compute_residual: 
ERROR: compute_residual (id=b3a8877311f35baf) returns an error.
ERROR: [compute_residual]: [0]: Executing script in Singularity returns an error (exitcode=-11, stderr=/restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/Covariate_data_preprocessing/batch_all_bam_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.ROSMAP_xqtl_covariates_sex_death_pmi_study.ROSMAP_NIA_WGS.leftnorm.filtered.related.filtered.extracted.pca.projected.resid.bed.gz.stderr).
The script has been saved to /usr4/bf527/skandoi/.sos/8df4c2d4d05f7817//usr4/bf527/skandoi/.sos/8df4c2d4d05f7817.To reproduce the error please run:
singularity exec  /restricted/projectnb/casa/xqtl-pipeline/container/singularity/bioinfo.sif Rscript /usr4/bf527/skandoi/.sos/8df4c2d4d05f7817/singularity_run_162946.R

*** caught segfault ***
address 0x7f22a4341901, cause 'invalid permissions'

R file:

/usr4/bf527/skandoi/.sos/8df4c2d4d05f7817/singularity_run_162946.R

library(dplyr)
library(readr)

pheno = read_delim('/restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/leafcutter_output/batch_all_bam_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.gz',delim = "\t")
covariate= read_delim('/restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/Covariate_data_preprocessing/ROSMAP_xqtl_covariates_sex_death_pmi_study.ROSMAP_NIA_WGS.leftnorm.filtered.related.filtered.extracted.pca.projected.gz',delim = "\t") 

# Extract samples in both files (Outliers will be removed in here as they are no longer presented in the header of factor)
extraction_sample_list <- intersect(colnames(pheno), colnames(covariate)) 

if(length(extraction_sample_list) == 0){
  stop("No samples are overlapped in two files!")
}

# Report identical samples:

print("Listed samples are included in the analysis:")
print(extraction_sample_list)

# Subset the data:
covariate = covariate[,extraction_sample_list]%>%as.matrix()%>%t()
pheno_id = pheno%>%select(1:4)
pheno = pheno%>%select(rownames(covariate))%>%as.matrix()%>%t()

# Get residual 
pheno_resid = .lm.fit(x = cbind(1,covariate), y = pheno)$residuals
pheno_output = cbind(pheno_id, pheno_resid%>%t())
pheno_output%>%write_delim("/restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/Covariate_data_preprocessing/batch_all_bam_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.ROSMAP_xqtl_covariates_sex_death_pmi_study.ROSMAP_NIA_WGS.leftnorm.filtered.related.filtered.extracted.pca.projected.resid.bed",delim = "\t")

[hsun3163]

*** caught segfault ***
address 0x7f22a4341901, cause 'invalid permissions'

Traceback:
 1: vroom_(file, delim = delim %||% col_types$delim, col_names = col_names,     col_types = col_types, id = id, skip = skip, col_select = col_select,     name_repair = .name_repair, na = na, quote = quote, trim_ws = trim_ws,     escape_double = escape_double, escape_backslash = escape_backslash,     comment = comment, skip_empty_rows = skip_empty_rows, locale = locale,     guess_max = guess_max, n_max = n_max, altrep = vroom_altrep(altrep),     num_threads = num_threads, progress = progress)
 2: vroom::vroom(file, delim = delim, col_names = col_names, col_types = col_types,     col_select = {        {            col_select        }    }, id = id, .name_repair = name_repair, skip = skip, n_max = n_max,     na = na, quote = quote, comment = comment, skip_empty_rows = skip_empty_rows,     trim_ws = trim_ws, escape_double = escape_double, escape_backslash = escape_backslash,     locale = locale, guess_max = guess_max, progress = progress,     altrep = lazy, show_col_types = show_col_types, num_threads = num_threads)
 3: read_delim("/restricted/projectnb/casa/skandoi/ROSMAP_DLPFC/leafcutter_output/batch_all_bam_intron_usage_perind.counts.gz_raw_data.qqnorm.formated.bed.gz",     delim = "\t")
An irrecoverable exception occurred. R is aborting now ...

The problem probably have to do with the inability to read this input file due to permission error

[hsun3163]

The similar error posted online seems to be from more complicated package instead of readr.