regex_error when extracting barcode

[May Ho]

Hello!

When I try executing this line of code:

bartender_extractor_com -f 2M_test.fq -o 2M_extracted -q ? -p TACC[4-7]AA[4-7]AA[4-7]TT[4-7]ATAA -m 2

I obtain this message:

2M_extracted 63 "(TAC.|TA.C|T.CC|.ACC)([ATCGN]{4,7})(AA)([ATCGN]{4,7})(AA)([ATCGN]{4,7})(TT)([ATCGN]{4,7})(ATA.|AT.A|A.AA|.TAA)" TACC ATAA 9 1  

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

  what():  regex_error

has anyone encountered this error before or do the authors know what might be happening here?

Thank you, 

May 

[赵路]

Hi May,

Thanks for using Bartender.

I suspect this problem is because of old gcc version. Upgrading it to latest version might just solve the problem. 

And also please download the latest bartender source code and build it by following README.

Please do share me the gcc version and operating system version no matter the problem is going away or not after the gcc upgrade.

Thanks

Lu 

[May Ho]

Hi Lu, 

Thanks for the prompt reply. The computer tech and I attempted to troubleshoot the problem by first upgrading the gcc version to 4.9 then we recompiled it. I re-ran the code and it was still giving me the same error. 

I'm executing the program on a server that's hosted on this operating system:

Centos Linux 7 as Operating System (it’s a RedHat derivat)

 

Operating System: CentOS Linux 7 (Core)

CPE OS Name: cpe:/o:centos:centos:7

Kernel: Linux 3.10.0-862.11.6.el7.x86_64

Architecture: x86-64

[赵路]

Hi May,

Sorry for the late reply. I could not reproduce the problem in my mac laptop. But I suspect this issue ties to the system environment. I noticed the same problem when using Bartender in old Ubuntu system when I migrated the Boost's regex lib to C++ regex lib. Unfortunately, I don't have any computer running in Centos and it would be a bit difficult for me to verify this. 

If possible, please re-run the same command under other system with latest gcc version. 

Thanks

Lu