terminate called after throwing an instance of 'std::logic_error'

[ptranvan]

Hi,

I have an issue after running merge_wrapper.py

4: FINISHING DATA
0       quickmerge
1       -d
2       out.rq.delta
3       -q
4       hybrid_oneline.fa
5       -r
6       self_oneline.fa
7       -hco
8       5.0
9       -c
10      1.5
11      -l
12      0
13      -ml
14      5000
terminate called after throwing an instance of 'std::logic_error'
  what():  basic_string::_M_construct null not valid

[esolares]

Hi Please try using the prefix option. I will be pushing a fix for setting a default prefix soon. Thank you, Edwin

…

On Wed, Oct 3, 2018, 1:36 PM Patrick Tran Van ***@***.***> wrote: Hi, I have an issue after running merge_wrapper.py 4: FINISHING DATA 0 quickmerge 1 -d 2 out.rq.delta 3 -q 4 hybrid_oneline.fa 5 -r 6 self_oneline.fa 7 -hco 8 5.0 9 -c 10 1.5 11 -l 12 0 13 -ml 14 5000 terminate called after throwing an instance of 'std::logic_error' what(): basic_string::_M_construct null not valid — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#35>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEI6vtOeHwCtL4eJf7mHsTPjsxaygtVjks5uhR9hgaJpZM4XG05P> .

[ptranvan]

This is my command:

merge_wrapper.py ../P1.fasta ../M1.fasta -pre P_query

And I still have the error

[FAFUyangyang]

i have the same question，I hope you can help me out，thank you。

[FAFUyangyang]

This is my command:

merge_wrapper.py ../P1.fasta ../M1.fasta -pre P_query

And I still have the error
Have you solved it？

[lfaller-zymergen]

Hello all,

I am encountering the same error. Please advise!

Best,
~Lina

[Joseph-Vineland]

I also have the same problem. I made sure to add quickmerge/mummer to my PATH.

export PATH=/mnt/nas/software/quickmerge:/mnt/nas/software/quickmerge/MUMmer3.23:$PATH

[mahulchak]

Did you try the quickmerge command line ? I think the problem is with the wrapper so while we fix it, you could try the quickmerge stand-alone version.

…

On Tue, Oct 30, 2018, 00:20 joneill4x ***@***.***> wrote: I also have the same problem. I made sure to add quickmerge/mummer to my PATH. export PATH=/mnt/nas/software/quickmerge:/mnt/nas/software/quickmerge/MUMmer3.23:$PATH — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#35 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHMD6ARq9CYlxJ9n8SnZIVQhdw4TFMQeks5up02qgaJpZM4XG05P> .

[jgbaldwinbrown]

Hi all,

I wrote the wrapper a while ago. I believe I have now fixed the merge_wrapper error. The problem was that quickmerge was modified to require a '-p' option to supply an output prefix, but the wrapper wasn't modified to send the wrapper's '-pre' prefix on to quickmerge. Take another crack at using the wrapper and let me know if it isn't working.

[Joseph-Vineland]

Thank you jgbaldwinbrown.

I would like to add, even though I added /the/path/to/quickmerge/MUMmer3.23/ to the $PATH variable, the version of MUMmer being called by the script was a 32 bit version.

I needed to do:

sudo apt-get purge mummer

Then place a 64 bit version of MUMmer in /usr/bin/ .

[jgbaldwinbrown]

It sounds like the problem is solved, and we got some useful advice about making sure that the 64-bit version of MUMmer is in use. I'm going to close this up.

[esolares]

Hi, If you source the file that is created when you compile quickmerge, you should have the 64bit version of MUMmer precede all other installations as it does: PATH=MYMUMPATH:$PATH where MYMUMPATH is the location where 64bit MUMmer is located. After compiling quickmerge you should get a line at the bottom telling you how to source the file. Also you can ls -al to see the file that needs to be sourced prior to running quickmerge. Please let us know if you have any more questions. Thank you, Edwin Solares, B.S. Computational Biology Department of Ecology and Evolutionary Biology Gaut Lab 5438 McGaugh Hall University of California, Irvine Irvine, CA 92697 USA

…

On Tue, Oct 30, 2018 at 1:03 PM joneill4x ***@***.***> wrote: Thank you jgbaldwinbrown. I would like to add, even though I added /the/path/to/quickmerge/MUMmer3.23/ to the $PATH variable, the version of MUMmer being called by the script was a 32 bit version. I needed to do: sudo apt-get purge mummer Then place a 64 bit version of MUMmer in /usr/bin/ . — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#35 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEI6vsccYkfaFAVW5jyOj5JzDBRNcwxrks5uqLAngaJpZM4XG05P> .