masurca icon indicating copy to clipboard operation
masurca copied to clipboard

jellyfish memory allocation error

Open nm100 opened this issue 6 years ago • 4 comments

FYI: estimated genome size is 2.2 Gb and coverage of illumina ~ 70X and PacBio coverage: ~14X

Getting memory allocation error below (using MaSuRCA v3.2.6) :

terminate called after throwing an instance of 'jellyfish::large_hash::array_base<jellyfish::mer_dna_ns::mer_base_static<unsigned long, 0>, unsigned long, atomic::gcc, jellyfish::large_hash::array<jellyfish::mer_dna_ns::mer_base_static<unsigned long, 0>, unsigned long, atomic::gcc, allocators::mmap> >::ErrorAllocation' what(): Failed to allocate 770000000000 bytes of memoryterminate called after throwing an instance of 'jellyfish::large_hash::array_base<jellyfish::mer_dna_ns::mer_base_static<unsigned long, 0>, unsigned long, atomic::gcc, jellyfish::large_hash::array<jellyfish::mer_dna_ns::mer_base_static<unsigned long, 0>, unsigned long, atomic::gcc, allocators::mmap> >::ErrorAllocation' what(): Failed to allocate 770000000000 bytes of memory ./assemble.sh: line 120: 59122 Aborted jellyfish count -m 31 -t 16 -C -s $JF_SIZE -o k_u_hash_0 pe.cor.fa sj.cor.fa Failed to open input file 'k_u_hash_0' Estimated genome size: Creating k-unitigs with k=99 ./assemble.sh: line 125: *2: syntax error: operand expected (error token is "*2") Creating k-unitigs with k=31 ./assemble.sh: line 130: *2: syntax error: operand expected (error token is "*2") Super reads failed, check super2.err and files in ./work2/

nm100 avatar May 10 '18 20:05 nm100

How much RAM do you have in your computer?

alekseyzimin avatar May 24 '18 18:05 alekseyzimin

I was running it on a cluster with ~1500 GB RAM

nm100 avatar May 24 '18 18:05 nm100

I have the same problem!

jiahao-liang avatar May 19 '21 11:05 jiahao-liang

Have you solved your problem yet? I met the same problem

lly1214 avatar Apr 18 '22 09:04 lly1214