mahulchak/svmu

segmentation fault

Closed this issue · 26 comments

Huanle commented

Hi There,

I ran into this error when execting svmu.
svmu ref.vs.sample.mm.delta ref.fa sample.fa 3
''
A little bit information about my linux platform:

Configured with: ../gcc-5.2.0/configure --prefix=/opt/Modules/gcc/5.2.0 --disable-multilib
Thread model: posix
gcc version 5.2.0 (GCC)

Linux delta040 2.6.32-573.12.1.el6.x86_64 #1 SMP Tue Dec 15 21:19:08 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

Hoepfully, you can show me a way to fix it.

Thanks a lot.

Elzed

mahulchak commented

Hi,
Could you please provide me the following information -

  1. exact error
  2. could you please run it again with /usr/bin/time -v
    i.e.
    /usr/bin/time -v svmu ref.vs.sample.mm.delta ref.fa sample.fa 3
    this will help me figure out if it is a memory issue. How big are your reference and sample sequences?
    -Mahul
Huanle commented

Hi Mahul,

Thanks for your prompt response.

What i got from running ' time svmu pun.vs.TOX.mm.delta pun.reformat.fa TOX.reformat.fa 4 '
is

"Segmentation fault
real 0m4.404s
user 0m4.092s
sys 0m0.143s
"

mahulchak commented
Huanle commented

Thanks.
$ /usr/bin/time svmu pun.vs.TOX.mm.delta pun.reformat.fa TOX.reformat.fa 4

0.42user 1.77system 0:02.33elapsed 94%CPU (0avgtext+0avgdata 680668maxresident)k
0inputs+8outputs (21major+170236minor)pagefaults 0swaps

sequence size:
TOX: 386,148,524
pun: 191,018,889

mahulchak commented
Huanle commented

128 GB.

mahulchak commented
BoWang12 commented

Hello, I ran svmu using my data, and I give it 300G memory, it was generating 'trans.txt' file, then got the segmentation fault error:
/var/spool/p6444/bnbhimem2/job_scripts/19840053: line 3: 37489 Segmentation fault ~/software/svmu/svmu ../split.job/sample.2ref.mm.delta ../ref.fa ../sample.fa 5
Could you give some suggestions? Thanks.

mahulchak commented
BoWang12 commented

Here is what I got using /usr/bin/time -v :

Command terminated by signal 11
Command being timed: "/sonas-hs/hpc/home/software/svmu/svmu ../split.job/sample.2ref.mm.delta ../ref.fa ../sample.fa 5"
User time (seconds): 704.88
System time (seconds): 23.49
Percent of CPU this job got: 99%
Elapsed (wall clock) time (h:mm:ss or m:ss): 12:10.15
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 132863040
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 6296558
Voluntary context switches: 59
Involuntary context switches: 78007
Swaps: 0
File system inputs: 0
File system outputs: 0
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0

mahulchak commented
BoWang12 commented

Yes, it created 'trans.txt', and this file is not empty, have some results inside, but no other files created

mahulchak commented
BoWang12 commented

Yes, it was a small file, which I used to test svmu

sample.2ref.mm.delta.txt

mahulchak commented

@Huanle I have pushed some new updates. Could you please check if it works now?

BoWang12 commented

Thanks for yoru help, I just tried the new updates, unfortunately seems still not working, here is what I got:
Command terminated by signal 11
Command being timed: "/sonas-hs/hpc/home/bwang/software/svmu/svmu ./sample.2ref.mm.delta ../ref.fa ./sample 5"
User time (seconds): 426.95
System time (seconds): 14.75
Percent of CPU this job got: 99%
Elapsed (wall clock) time (h:mm:ss or m:ss): 7:22.45
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 91573440
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 3715444
Voluntary context switches: 24
Involuntary context switches: 45528
Swaps: 0
File system inputs: 0
File system outputs: 0
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0

BoWang12 commented

I'm sharing my data files with you through dropbox, could you test on your side? see how it goes. Thanks. Here is the link: https://www.dropbox.com/sh/23ewo64ykicj8un/AADKhyLRjCHxr4wmZ_fNYFJwa?dl=0

BoWang12 commented

Hello, I was wondering have you figured out the problem? Thanks.

mahulchak commented

I have located the problem but I haven't had time to fix it. I plan to do it in the next couple of days. Sorry for the delay.

mahulchak commented

@BoWang12 sorry for the delay. The problem should now be solved.

situssog commented

Hello Mahul,

I'm also trying to run the package but I'm getting the same problem. It runs, produces part of the trans file, and stops with the message: Segmentation fault (core dumped)

the command:
/usr/bin/time -v svmu svmu_ref.delta Ref.fasta sample.fasta 10

Command terminated by signal 11
Command being timed: "svmu svmu_ref.delta Ref.fasta sample.fasta 10"
User time (seconds): 76.08
System time (seconds): 2.69
Percent of CPU this job got: 99%
Elapsed (wall clock) time (h:mm:ss or m:ss): 1:18.99
Average shared text size (kbytes): 0
Average unshared data size (kbytes): 0
Average stack size (kbytes): 0
Average total size (kbytes): 0
Maximum resident set size (kbytes): 4447332
Average resident set size (kbytes): 0
Major (requiring I/O) page faults: 0
Minor (reclaiming a frame) page faults: 1215104
Voluntary context switches: 58
Involuntary context switches: 48888
Swaps: 0
File system inputs: 0
File system outputs: 56
Socket messages sent: 0
Socket messages received: 0
Signals delivered: 0
Page size (bytes): 4096
Exit status: 0

I'm wondering if this is a compilation problem or if this is a general problem others are having.
My input files are here:
https://www.dropbox.com/sh/0bljkelodsxfuju/AADfXfX9iGULk-VCQPhSbjJna?dl=0

Thanks a lot for your help,

/S

mahulchak commented

@situssog Thanks for letting me know and sharing the files. I will take a look.

mahulchak commented

@situssog I am unable to replicate your error. You'll need 4Gb RAM to run this. It's also possible that you don't have the latest version. I will commit some changes today or tomorrow and then you can check it again.

situssog commented

Hello Mahul,

Thanks a lot for your quick reply.
I allocated 24 Gb to the job in the cluster. After trying several things I notice the problem was the name of the sequences in the sample.fasta file (apparently too long). Is there a max number of characters in the seq name? Is tehre a way to change these settings?

After changing names to a very simple one (For instance to >ABCD) the package runs.

Now, my output files do not show mitochondrial SVs. Is this because of the length of the sequence? Can I change something in the MUMmer run to get them?

Thanks a lot for your help,

/S

situssog commented

Hello Mahul,
Sorry for the multiple consecutive messages. Now I notice that if I reduce the n parameter (from 5 to 2 or even 1/0), I do get the MT SV. However, this is always not the case and in some cases, I don't get SV from large chromosomes. Link to input files as example:

https://www.dropbox.com/sh/0bljkelodsxfuju/AADfXfX9iGULk-VCQPhSbjJna?dl=0

This a link to the alignment of that sample and the reference:
http://qb.cshl.edu/assemblytics/interactive_dotplot.php?code=aYmv37WbPdJ9MMZn6uVK&nickname=my_favorite_organism

If I run MUMmer using the -mumreference parameter, I get more chromosomes, but for instance chromosome III only shows one out of two contigs.

Thanks a lot again,

/S

mahulchak commented

@situssog I am sorry but I am unable to replicate any of the errors you are mentioning. I have updated the code with some new commits. Please check if they solve the issues you are having. I looked for all reference chromosomes in sv.txt and found all of them. The commands I have used :

nucmer -maxmatch -noextend Ref.fasta sample.fasta 
/usr/bin/time -v ./svmu sample2ref.delta ref.fasta sample.fasta 1 l

l is a new parameter. Please see svmu updated README for its description.