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smithlabcode / methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.
http://smithlabresearch.org/methpipe
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radmeth adjust - "Core Dumped" #204

Closed Mazklaus closed 1 year ago

Mazklaus commented 2 years ago

Hello,

I am working with methpipe for processing Whole Genome Bisulfite Sequencing data. Since, the mapping and methylation extraction is handle in my lab by other means I planned to only use the radmeth part to process a differential analysis of our samples.

I followed the methpipe documentation, using first the merge-methcounts ALL_MY_FILES > proportion_table.txt to generate the proportion table without trouble.

Then I used radmeth regression -factor case design_matrix.txt proportion_table.txt > cpgs.bed with the design_matrix_file as follow :

base case
C002DKK_1.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DKL_1.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DKM_1.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DKN_1.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DKO_1.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DKP_1.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DKQ_1.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DKR_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DKS_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DKT_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DKU_1.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DKV_1.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DKW_1.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DKX_1.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DKY_1.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DKZ_1.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DL2_1.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DL3_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DL4_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DL5_FHB_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DL7_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DL8_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DL9_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DLA_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1  0
C002DLB_FHB_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DLC_FHB_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DLD_FHB_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DLE_FHB_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DLF_FHB_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 0
C002DLG_FHB_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DLH_FHB_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DLI_FHB_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DLJ_FHB_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DLK_FHB_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DLL_FHB_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DLM_FHB_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DLN_FHB_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DLO_FHB_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1
C002DLP_FHB_all.merged.cov.CpG_report.merged_CpG_evidence.meth 1 1

It has run without trouble giving a cpgs.bed file lookink like this :

chr1    3000827 +       CpG     0.244919        432     311     525     432
chr1    3001007 +       CpG     0.320374        432     340     454     372
chr1    3001018 +       CpG     0.144045        439     356     454     342
chr1    3001277 +       CpG     0.262408        312     166     316     154
chr1    3001629 +       CpG     0.00562261      450     357     451     322
chr1    3003226 +       CpG     0.233117        141     91      196     95
chr1    3003339 +       CpG     0.608708        317     250     395     263
chr1    3003379 +       CpG     0.1565  326     239     402     314
chr1    3003582 +       CpG     0.023006        281     206     343     141
chr1    3003640 +       CpG     0.793321        104     131     143     57

My problem occur when i try to run the adjustment proposed by radmeth. Using radmeth adjust -bins 1:200:1 cpgs.bed > cpgs.adjusted.bed the script instantly crash with a "core dumped" error leaving only the following log in the "cpgs.adjusted.bed" :

/env/products/gcc/9.2.0/include/c++/9.2.0/bits/stl_vector.h:1042: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](std::vector<_Tp, _Alloc>::size_type) [with _Tp = std::vector<double>; _Alloc = std::allocator<std::vector<double> >; std::vector<_Tp, _Alloc>::reference = std::vector<double>&; std::vector<_Tp, _Alloc>::size_type = long unsigned int]: Assertion '__builtin_expect(__n < this->size(), true)' failed.

I wasn't able to figure out if I am doing something wrong when i call the script or if there is an error in the code.

Could you please help me understand what happens ?

NB : I am working on a slurm cluster, giving 32 cpus and 10Go of memory per cpus to run the job.

guilhermesena1 commented 2 years ago

Hello,

If you're still having the issue, would you be able to either share the cpgs.bed file or the smallest file on which the issue still occurs? From the error message itself it's hard to tell if it's a code problem or a resource problem, but we definitely should be providing a more informative error message.

andrewdavidsmith commented 1 year ago

Closing due to inactivity.