I have a dataset of 130 WGR samples but it keeps
getting ‘Killed’ in the middle of SNP calling. A similar issue previously posted suggested a problem with either the code or the bam files which I then investigate. I have reduced the sample size to 2 samples and reran the code. The process finished successfully. I then investigate the issues with the bam files. I have run multiple set of 50 with different samples and they all successfully finished. The ‘Killed’ error appeared again when I increase the sample size to 75.
Here is my code and an example of the error:
angsd -doMaf 2 -GL 1 -doMajorMinor 1 -bam bam.filelist -out SNPcalling_Trial1 -SNP_pval 1e-6 -minMapQ 30 -minQ 30 -uniqueOnly 1 -remove_bads 1 -only_proper_pairs 1 -minMaf 0.05 -minInd 120 -setMinDepthInd 5 -geno_mindepth 5
I get the result that the run is killed
-> angsd version: 0.933 (htslib: 1.9) build(May 6 2020 21:25:11) -> NB: you are doing qscore distribution, set -minQ to zero if you want to count qscores below: 30 -> SNP-filter using a pvalue: 1.000000e-06 correspond to 23.928127 likelihood units [bammer_main] 130 samples in 135 input files -> Parsing 130 number of samples -> Allocated ~ 10 million nodes to the nodepool, this is not an estimate of the memory usage -- -> Allocated ~ 190 million nodes to the nodepool, this is not an estimate of the memory usage -> Printing at chr: scaffold_81380 pos:134963 chunknumber 1840400 contains 461 sites are killed
I have running on a linux with a ulimit -n of 1024. Is it a memory issue? Please advise on how to proceed. Thanks!