Possible solution to 'core dumped' error?

[javibio-git]

Hello,

I am trying to run svmu for three drosophila genomes and I am following the basic instructions posted on this repository. I tried several times to run svmu but the jobs were always aborted and showing a 'core dumped error'. Then I looked at the stderr file and this message was printed:

terminate called after throwing an instance of 'std::invalid_argument'
  what():  stoi

The 'invalid_argument' error made me think that maybe I was not specifying the correct number/format of arguments. Then I noticed that in the basic running instructions only 6 arguments are needed to run svmu:

svmu sam2ref.mm.delta ref.fasta sample.fasta snp_mode sam_lastz.txt prefix

But when I executed svmu with no arguments it gives me:

Usage: /media/DATA5/Javier/software/svmu/svmu_exp/svmu/svmu foo.delta ref.fasta query.fasta cutoff mode(h/l) last_out.txt prefix

As you can see, the binary itself asks for 7 arguments by asking also for a cutoff parameter. I remember from an old version that there was a parameter for the number of unique syntenic blocks to find SVs, which can take values of 5, 10 or 100. I ended up running something like this and It seems that svmu is running:

svmu delta_file reference.fasta target.fasta 5 l lastz_out.txt prefix

Now my questions are: Do you think the parameters 'cutoff' and 'mode' and the way I put them in my command line were correct for the proper function of svmu? Are those actually taken into consideration?

Looking forward to hearing back from you.

Javier,

[mahulchak]

Hi Javier, apologies for the confusion. I should update the command description on GitHub. Yes, you are running it correctly.

On Thu, Jul 16, 2020 at 7:41 AM javbioUMD notifications@github.com wrote:

Hello,

I am trying to run svmu for three drosophila genomes and I am following the basic instructions posted on this repository. I tried several times to run svmu but the jobs were always aborted and showing a 'core dumped error'. Then I looked at the stderr file and this message was printed:

terminate called after throwing an instance of 'std::invalid_argument' what(): stoi

The 'invalid_argument' error made me think that maybe I was not specifying the correct number/format of arguments. Then I noticed that in the basic running instructions only 6 arguments are needed to run svmu:

svmu sam2ref.mm.delta ref.fasta sample.fasta snp_mode sam_lastz.txt prefix

But when I executed svmu with no arguments it gives me:

Usage: /media/DATA5/Javier/software/svmu/svmu_exp/svmu/svmu foo.delta ref.fasta query.fasta cutoff mode(h/l) last_out.txt prefix

As you can see, the binary itself asks for 7 arguments by asking also for a cutoff parameter. I remember from an old version that there was a parameter for the number of unique syntenic blocks to find SVs, which can take values of 5, 10 or 100. I ended up running something like this and It seems that svmu is running:

svmu delta_file reference.fasta target.fasta 5 l lastz_out.txt prefix

Now my questions are: Do you think the parameters 'cutoff' and 'mode' and the way I put them in my command line were correct for the proper function of svmu? Are those actually taken into consideration?

Looking forward to hearing back from you.

Javier,

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-- Mahul Chakraborty Department of Ecology and Evolutionary Biology University of California-Irvine Phone: 949 824 9559 Fax: 949 824 9559 Website: https://mahulchakraborty.wordpress.com/ Github: https://github.com/mahulchak

[javibio-git]

Thank you a lot for the clarification.

Do the cutoff and the mode parameters are taken into consideration?

Thank you.

Javier

[mahulchak]

cutoff is not used anymore. I would recommend keeping the mode as 'l'

On Fri, Jul 17, 2020 at 8:48 AM javbioUMD notifications@github.com wrote:

Thank you a lot for the clarification.

Do the cutoff and the mode parameters are taken into consideration?

Thank you.

Javier

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/mahulchak/svmu/issues/12#issuecomment-660178230, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZQH2ABEOTBNE4VRWYVV73R4BWOLANCNFSM4O4LYQDQ .

-- Mahul Chakraborty Department of Ecology and Evolutionary Biology University of California-Irvine Phone: 949 824 9559 Fax: 949 824 9559 Website: https://mahulchakraborty.wordpress.com/ Github: https://github.com/mahulchak

[javibio-git]

Thank you!