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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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graphmap terminate called after throwing an instance of 'std::bad_alloc' #49

Closed mdcao closed 7 years ago

mdcao commented 7 years ago

Hi Ivan, In a few instances, graphmap throws the error "terminate called after throwing an instance of 'std::bad_alloc'". Error message:

[03:40:52 ProcessReads] [CPU time: 207530.06 sec, RSS: 108099 MB] Read: 40255/93606 (43.00%) [m: 33162, u: 7082], length = 26, qname: 6ab83d51-3dbe-4d6c-ba2a-67... [03:40:52 ProcessReads] [CPU time: 207530.06 sec, RSS: 108104 MB] Read: 40256/93606 (43.01%) [m: 33162, u: 7083], length = 49, qname: 88a881ee-0e1e-4939-adca-ed... [03:40:52 ProcessReads] [CPU time: 207530.08 sec, RSS: 108115 MB] Read: 40257/93606 (43.01%) [m: 33162, u: 7084], length = 140, qname: 672cd3c8-990d-4aea-b32d-8... [03:40:54 ProcessReads] [CPU time: 207543.75 sec, RSS: 110695 MB] Read: 40293/93606 (43.05%) [m: 33162, u: 7120], length = 19, qname: db403299-d52f-4bf9-a8c8-91... [03:40:54 ProcessReads] [CPU time: 207543.77 sec, RSS: 110699 MB] Read: 40294/93606 (43.05%) [m: 33162, u: 7121], length = 106, qname: 3cef43ed-3d26-4e54-9a04-0...terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc

Can you have a look to see how can we avoid these? Thanks

isovic commented 7 years ago

Hi, thank you for the report! Which commit are you using? Also, how much RAM does your system have?

Best regards, Ivan.

mdcao commented 7 years ago

Hi Ivan, Thank for having a look. I use version graphmap v0.3.2. I used PBS and allocated 120GB of memory for the job. Let me allocate more memory to see if that solve the problem. Thanks

mdcao commented 7 years ago

Hi Ivan, allocating more memory (160GB) did solve the problem. Thanks

isovic commented 7 years ago

Great, thanks! I would only suggest to update GraphMap to the latest version.

Best regards, Ivan.

lwratten commented 4 years ago

Hello, I am having a similar issue. Is there an option to specify the RAM as a command line flag? Thanks!