rxstacks terminate called after throwing an instance of 'std::regex_error'

[ty...@baumannlab.org]

Stacks user group,

I'm trying to run rxstacks on a couple different data sets. However, regardless of the rxstacks command (I've provided 3 examples) I use I get the following error:

1. tfording@bonsai /n/projects/tfording/hybridogenesis/data/samples/v6_combinedData/marm_masked_map/stacks_diploid_mother$ rxstacks -b 9 -P /n/projects/tfording/hybridogenesis/data/samples/v6_combinedData/marm_masked_map/stacks_diploid_mother/ -o /n/projects/tfording/hybridogenesis/data/samples/v6_combinedData/marm_masked_map/stacks_diploid_mother/corr --conf_lim 0.25 --prune_haplo --model_type bounded --bound_high 0.1 --lnl_lim --lnl_dist 

terminate called after throwing an instance of 'std::regex_error'
what(): regex_error
Aborted


2. tfording@bonsai /n/projects/tfording/hybridogenesis/data/samples/v6_combinedData/marm_masked_map/stacks_diploid_mother$ rxstacks -v

terminate called after throwing an instance of 'std::regex_error'
what(): regex_error
Aborted


3. tfording@bonsai /n/projects/tfording/hybridogenesis/data/samples/v6_combinedData/marm_masked_map/stacks_diploid_mother$ rxstacks

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

what(): regex_error

Aborted

I ran rxstacks without issue a couple weeks ago, and initially assumed something went wrong with my installation. I uninstalled and reinstalled via Anaconda, and get the same error. 

Thanks for your help,

Tyler

[Stephen Hauskins]

As a quick response the error involves regex (Regular Expressions) and I see in every command line

that you have a "$" that is a regular expressions  which means The match must occur at the end of the string or before \n at the end of the line or string.

Are you trying to use a wildcard to match data files?

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Stephen Hauskins
Purveyor of fine computing services

831-334-3961

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[ty...@baumannlab.org]

Stephen,

That is simply the end of my shell prompt line. The actual command for rxstacks starts immediately after that. The $ shouldn't be viewed by the program as far as I'm aware.

Tyler

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[ty...@baumannlab.org]

Update:

I tried installing Stacks without Anaconda and when I run the ./configure command it throws the following error:

checking for functional regular expressions... configure: error: Regular expressions are not functional, you need g++ 4.9.0 or greater.

It seems my version of gcc/g++ isn't correct anymore. Anaconda's most recent version is 4.8.5. Is there a way to install this dependency without "sudo"? If not, I'll have to request the install through our admins.

Thanks,

Tyler 

[Nicolas Rochette]

Hi Tyler,

Yes, this error is characteristic of GCC 4.8. This version ships with regex libraries that compile just fine but commit sucide as soon as you try to use them.

I would recommend asking the admins to update the system. GCC is a core part of any system, and even 4.9 is very old already.

Best,

Nicolas

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[ty...@baumannlab.org]

Thanks for your help Nicolas!