segmentation fault

[Huanle]

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]

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]

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]

Please run /usr/bin/time -v svmu And not time svmu Also, could you please tell me your sequence sizes ?

On Thu, Dec 7, 2017, 17:58 HUANLE notifications@github.com wrote:

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 "

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[Huanle]

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]

How much memory does your system have ?

On Thu, Dec 7, 2017, 20:38 HUANLE notifications@github.com wrote:

$ /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

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[Huanle]

128 GB.

[mahulchak]

Okay. I'll push some updates on github tomorrow. Try that and let me know if you get the segfault.

On Sun, Dec 10, 2017, 14:57 HUANLE notifications@github.com wrote:

128 GB.

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[BoWang12]

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]

Could you please run svmu with /usr/bin/time -v

So that I know how much memory was being used when it crashed.

On Wed, Dec 13, 2017, 15:11 Bo Wang notifications@github.com wrote:

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.

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[BoWang12]

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]

Hmm. And you said it created the trans.txt file but didn't write anything to it? Did it create any other file?

On Wed, Dec 13, 2017, 17:51 Bo Wang notifications@github.com wrote:

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

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[BoWang12]

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

[mahulchak]

Will you be able to share your delta file ?

On Wed, Dec 13, 2017, 18:23 Bo Wang notifications@github.com wrote:

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

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[BoWang12]

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

sample.2ref.mm.delta.txt

[mahulchak]

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

[BoWang12]

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]

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]

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

[mahulchak]

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]

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

[situssog]

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]

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

[mahulchak]

@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]

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]

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]

@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.