alekseyzimin / masurca

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jellyfish memory allocation error #23

Open nm100 opened 6 years ago

nm100 commented 6 years ago

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/

alekseyzimin commented 6 years ago

How much RAM do you have in your computer?

nm100 commented 6 years ago

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

jiahao-liang commented 3 years ago

I have the same problem!

lly1214 commented 2 years ago

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