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std::bad_alloc #2
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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
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Sujun Li
Assistant Principal Scientist
School of Informatics and Computing
Lindley Hall
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Bloomington, IN 47405-7104
Email: Sujli@indiana.edu lisujun@gmail.com
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Hi Sujun, The Graph file comes from Metaspades (i didn't process it in any way) and the size is 56Mb Thank you very much for your help! Benoit |
Hello, Do you guys have an idea about that? Should I modify the graph somehow to be able to use it? |
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
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Hello, Sure I can do that. Should I send that by email? Benoit |
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
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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, |
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
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Sent! Ben |
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
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Were you able to fix this? I am trying to use this tool and ran into the same error. |
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.
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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
|
Hello,
I'm trying to run Graph2Pro and I came into this issue:
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
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