search

bcgsc / arks

ARCHIVED 🌈Alignment-free scaffolding of genome assemblies with 10x Genomics Chromium reads. ARCS/ARKS projects have been consolidated: https://github.com/bcgsc/arcs
10 stars 3 forks source link

Perl library error #25

Closed apn83 closed 4 years ago

apn83 commented 5 years ago

Hi, I am using a cluster which has common software installations. I am trying to make a pipeline with LR_gapcloser and ARKS for 3 rounds. LR_gapcloser uses, perl-5.26.1. I am not sure, what version does ARKS use. Because, after LR_gapcloser completes, arks stops before creating scaffolds.fa. The error I get is:

/usr/bin/perl: symbol lookup error: /sw/csi/perl/5.26.1/el7_gnu6.4.0/lib/site_perl/5.26.1/x86_64-linux-thread-multi/auto/Cwd/Cwd.so: undefined symbol: Perl_xs_handshake make: *** [R1_c5_m50-10000_k30_r0.05_e30000_z500_l5_a0.3.scaffolds.fa] Error 127

Please let me know about a solution to fix this. Thanks.

lcoombe commented 5 years ago

Hi @gitarunprasanna83,

Have you been able to test your LINKS installation? (Based on the perl error, I'm assuming that this error happened on the LINKS step).

Do you have multiple versions of perl installed on your server? I haven't come across that particular error before, but some issues online suggest it could be due to using a library that was compiled for a different perl than the one you are using. (https://stackoverflow.com/questions/44402544/taxid2wgs-pl-undefined-symbol-perl-xs-handshake, https://stackoverflow.com/questions/20407963/switch-to-different-version-of-perl-modules-version)

Lauren

lcoombe commented 4 years ago

Closing this issue due to inactivity -- feel free to re-open if you still have questions.