std::bad_alloc

[KunathBJ]

Hello,

I'm trying to run Graph2Pro and I came into this issue:

Now read graph from file /mnt/users/benoitk/Graph2prot/Graph2Pro-master/assembly_graph.fastg
num edge to be allocated: -1645797128
num_vertex to be allocated: 1003373042
num_vertex actually extracted: 2
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
/var/tmp/slurmd/job8873338/slurm_script: line 19: 27773 Aborted (core dumped) $P3/./DBGraph2Pro -e $P0/assembly_graph.fastg -s $P0/contigs.fasta -o $P0/contig-pep.fasta

After a bit of google search, it seems that It might be a memory issues.
Could you confirm me that it's the case and if yes, do you know how much memory I should use?

Thank a lot!
Best regards,
Benoit

[lisujun]

Hi, Benoit, It looks like something wrong with the fastg format. How big is the graph ? what is the kmer size when you construct the graph ? Thanks much. Best Sujun

…

On Fri, Dec 15, 2017 at 7:27 AM, KunathBJ ***@***.***> wrote: Hello, I'm trying to run Graph2Pro and I came into this issue: Now read graph from file /mnt/users/benoitk/Graph2prot/ Graph2Pro-master/assembly_graph.fastg num edge to be allocated: -1645797128 num_vertex to be allocated: 1003373042 num_vertex actually extracted: 2 terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc /var/tmp/slurmd/job8873338/slurm_script: line 19: 27773 Aborted (core dumped) $P3/./DBGraph2Pro -e $P0/assembly_graph.fastg -s $P0/contigs.fasta -o $P0/contig-pep.fasta After a bit of google search, it seems that It might be a memory issues. Could you confirm me that it's the case and if yes, do you know how much memory I should use? Thank a lot! Best regards, Benoit — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AK43L9rYpJU18L1QrmVR1lQCKhBXOu7dks5tAmWjgaJpZM4RDarV> .

-- Sujun Li Assistant Principal Scientist School of Informatics and Computing Lindley Hall 150 S. Woodlawn Avenue Bloomington, IN 47405-7104 Email: Sujli@indiana.edu lisujun@gmail.com

[KunathBJ]

Hi Sujun,

The Graph file comes from Metaspades (i didn't process it in any way) and the size is 56Mb
I used a set of kmers: 21,33,55,77 and used the final contigs and graph file produced by Metaspades.

Thank you very much for your help!
Best,

Benoit

[KunathBJ]

Hello,

Do you guys have an idea about that? Should I modify the graph somehow to be able to use it?
Best
Benoit

[lisujun]

Hi Benoit, Would you please share the fastg with us ? Sometimes the format has some issues that we have to take a look and modify the code accordingly ? Thanks much

…

Sent from my iPhone

On Dec 19, 2017, at 06:50, KunathBJ ***@***.***> wrote: Hello, Do you guys have an idea about that? Should I modify the graph somehow to be able to use it? Best Benoit — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[KunathBJ]

Hello,

Sure I can do that. Should I send that by email?
Thanks a lot

Benoit

[lisujun]

It is probably very big, right ? Can you share a google doc with me ?

…

Sent from my iPhone

On Dec 19, 2017, at 09:53, KunathBJ ***@***.***> wrote: Hello, Sure I can do that. Should I send that by email? Thanks a lot Benoit — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[KunathBJ]

Yes of course. But I thought I needed an e-mail to share the folder (couldn't find your e-mail though) or do you want me to put the link here?

Best,
Benoit

[lisujun]

My email address is lisujun@gmail.com

…

Sent from my iPhone

On Dec 19, 2017, at 11:32, KunathBJ ***@***.***> wrote: Yes of course. But I thought I needed an e-mail to share the folder (couldn't find your e-mail though) or do you want me to put the link here? Best, Benoit — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[KunathBJ]

Sent!
Thanks a lot for the help

Ben

[lisujun]

I will be out of town but work slowly. We will definitely get back to you. Thanks much

…

Sent from my iPhone

On Dec 19, 2017, at 11:48, KunathBJ ***@***.***> wrote: Sent! Thanks a lot for the help Ben — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[maguileraf]

Were you able to fix this? I am trying to use this tool and ran into the same error.

[lisujun]

Hi, Can you use this repository : https://github.com/COL-IU/graph2pro-var We updated to another version. maguileraf <notifications@github.com> 于2019年4月26日周五 下午2:20写道：

…

Were you able to fix this? I am trying to use this tool and ran into the same error. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACXDOLYKVIHTMV6ZLAIFWH3PSNBWHANCNFSM4EINVLKQ> .

-- Sujun Li Assistant Principal Scientist School of Informatics and Computing Lindley Hall 150 S. Woodlawn Avenue Bloomington, IN 47405-7104 Email: Sujli@indiana.edu lisujun@gmail.com