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Old 04-25-2012, 07:56 AM   #1
jjjscuedu
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Location: NY

Join Date: Mar 2012
Posts: 35
Default 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
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Old 05-07-2012, 02:02 AM   #2
BenjaminL
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Location: Hartford, CT

Join Date: Sep 2010
Posts: 5
Default 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?
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Jackson Laboratory for Genomic Medicine
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