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isovic / graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/graphmap2
MIT License
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Core Dumped - v0.5.0 #57

Closed Nilad closed 7 years ago

Nilad commented 7 years ago

Hi, i run graphmap with a fresh clone of your github (today) and i have this core dump. I work with others mappers with the same file for genome reference and fastq.

Cmd line :

graphmap align -t 8 -r mygenome.fasta -d myFastq.fastq -o myOutput.sam

Error :

[09:24:46 BuildIndexes] Loading reference sequences. [09:25:21 SetupIndex_] Building the index for shape: '11110111101111'. terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped)

If you need complementary information, i am at your disposition.

isovic commented 7 years ago

Hi, how big is your reference, and how much RAM does your machine have? Currently, building the index peaks at 32x reference_size (in bytes), but this will be reduced significantly in the next release.

Best regards, Ivan.

Nilad commented 7 years ago

I have 48Go of RAM for a genome reference of 2.6Go.

isovic commented 7 years ago

Unfortunately that won't be enough to build the index...do you have access to a higher-mem machine where you could build the index and transfer locally? Once build, the index will consume only about ~20GB. This will be patched up in the next release.

Best regards, Ivan.

Nilad commented 7 years ago

Thank you for your support.

I launch on an another machine (177Go RAM), it's take 90Go of RAM. I hope you can optimize the RAM cost of graphmap soon.