Dsuite Dinvestigate error but no indication as to the source
0
0
Entering edit mode
7 weeks ago
Drew • 0

Can anyone tell me what this error code is saying?

There are 3 sets (populations/species) excluding the Outgroup
/builddir/build/BUILD/gcc-11.4.1-20230605/obj-x86_64-redhat-linux/x86_64-redhat-linux/libstdc++-v3/include/bits/basic_string.h:1040: std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::const_reference std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator[](std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type) const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::const_reference = const char&; std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type = long unsigned int]: Assertion '__pos <= size()' failed.
Aborted (core dumped)

There is no indication as to what is causing this problem. I can run the program just fine with the tutorial data, so it clearly is not a problem with the installation. I'm assuming that this is an issue with something in my actual vcf. I have tried many different filter/vcf modification steps to try and address this, but nothing works.

I can provide more information as needed.

Any help would be greatly appreciated.

Dsuite • 376 views
ADD COMMENT
0
Entering edit mode

Aborted (core dumped) usually happens from a lack of resources. Are you running this on a local machine or a HPC node?

ADD REPLY
0
Entering edit mode

I am running on an interactive HPC node. I thought the 'Aborted (core dumped)' was due to the line of text just above it.

Also, there is no problem when I run the tutorial vcf dataset on the interactive node.

ADD REPLY
0
Entering edit mode

Demo files are designed to consume minuscule resources. Make sure you're giving the task as much RAM as it needs.

ADD REPLY
0
Entering edit mode

Memory was not the issue. After a lot of manually investigating my vcf file, I found that to be the issue. Once the issue was fixed, then I was able to complete it on an interactive node and as a batch job. The aborted core dumped was just a product of the program stopping.

ADD REPLY

Login before adding your answer.

Traffic: 2566 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6