Perl library error
Closed this issue · 2 comments
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.
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
Closing this issue due to inactivity -- feel free to re-open if you still have questions.