trinity error

jjjscuedu · 04-25-2012, 07:56 AM

I try to run the trinity for my RNA-seq dataset, but get the following errors:

CMD finished (0 seconds)
CMD: /diag/software/trinityrnaseq_r2012-03-17/Inchworm/bin/inchworm --kmers meryl.kmers.min1.fa --run_inchworm -K 25 -L 48 --monitor 1 > /diag/home/jjin/rice/leaf/test/inchworm.K25.L48.fa.tmp
/diag/software/trinityrnaseq_r2012-03-17/Inchworm/bin/inchworm: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /diag/software/trinityrnaseq_r2012-03-17/Inchworm/bin/inchworm)
/diag/software/trinityrnaseq_r2012-03-17/Inchworm/bin/inchworm: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /diag/software/trinityrnaseq_r2012-03-17/Inchworm/bin/inchworm)
Error, cmd: /diag/software/trinityrnaseq_r2012-03-17/Inchworm/bin/inchworm --kmers meryl.kmers.min1.fa --run_inchworm -K 25 -L 48 --monitor 1 > /diag/home/jjin/rice/leaf/test/inchworm.K25.L48.fa.tmp died with ret 256 at /diag/software/trinityrnaseq_r2012-03-17/Trinity.pl line 1092.

** The inchworm process failed. Below is the tail end of the log file:

I don't know why i get this error.
Can anysone give me some suggestions?

Jingjing

BenjaminL · 05-07-2012, 02:02 AM

Hallo Jingjing!

> /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found

means that the inchworm application is missing a library of the required version. This is a standard system library used for running applications written in c++.

Most likely the app needs to be recompiled on your system. Or if there is a configuration file, shell variables, etc. that can be changed to match the location of your library files, then that could work.

Did you compile inchworm on your machine, or download it pre-compiled?

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04-25-2012, 07:56 AM	#1
jjjscuedu Member Location: NY Join Date: Mar 2012 Posts: 30	trinity error I try to run the trinity for my RNA-seq dataset, but get the following errors: CMD finished (0 seconds) CMD: /diag/software/trinityrnaseq_r2012-03-17/Inchworm/bin/inchworm --kmers meryl.kmers.min1.fa --run_inchworm -K 25 -L 48 --monitor 1 > /diag/home/jjin/rice/leaf/test/inchworm.K25.L48.fa.tmp /diag/software/trinityrnaseq_r2012-03-17/Inchworm/bin/inchworm: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /diag/software/trinityrnaseq_r2012-03-17/Inchworm/bin/inchworm) /diag/software/trinityrnaseq_r2012-03-17/Inchworm/bin/inchworm: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /diag/software/trinityrnaseq_r2012-03-17/Inchworm/bin/inchworm) Error, cmd: /diag/software/trinityrnaseq_r2012-03-17/Inchworm/bin/inchworm --kmers meryl.kmers.min1.fa --run_inchworm -K 25 -L 48 --monitor 1 > /diag/home/jjin/rice/leaf/test/inchworm.K25.L48.fa.tmp died with ret 256 at /diag/software/trinityrnaseq_r2012-03-17/Trinity.pl line 1092. ** The inchworm process failed. Below is the tail end of the log file: I don't know why i get this error. Can anysone give me some suggestions? Jingjing

05-07-2012, 02:02 AM	#2
BenjaminL Junior Member Location: Deustchland Join Date: Sep 2010 Posts: 5	compilation errors Hallo Jingjing! > /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found means that the inchworm application is missing a library of the required version. This is a standard system library used for running applications written in c++. Most likely the app needs to be recompiled on your system. Or if there is a configuration file, shell variables, etc. that can be changed to match the location of your library files, then that could work. Did you compile inchworm on your machine, or download it pre-compiled? __________________ Benjamin BioInformatiker Universitätsklinikum Münster