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Memory error when using metasv

Open daxian248 opened this issue 6 years ago • 9 comments

I'm using metasv to merge the output of pindel, cnvnator and breakdancer. But I get the error "OSError: [Errno 12] Cannot allocate memory". I want to know if the metasv read all the bam file into memory when merge the SVs. Here is my command: run_metasv.py --reference /public/home/ylma/genome/Sus_scrofa/Sus_scrofa.Sscrofa10.2.dna.toplevel.fa
--breakdancer_native rc.out
--cnvnator_native rc.cnv
--pindel_native rc_D rc_LI rc_SI rc_TD rc_INV
--sample BMX --bams SAMN02298127.02.bam SAMN02298128.02.bam SAMN02298129.02.bam SAMN02298130.02.bam SAMN02298131.02.bam SAMN02298132.02.bam
--spades /public/home/ylma/tools/SPAdes-3.10.1-Linux/bin/spades.py
--age /public/home/ylma/tools/AGE/age_align --num_threads 15 --workdir work --outdir out
--max_ins_intervals 500000 --isize_mean 500 --isize_sd 150

daxian248 avatar Oct 17 '17 08:10 daxian248