Go Back   SEQanswers > Applications Forums > De novo discovery

Similar Threads
Thread Thread Starter Forum Replies Last Post
Trinity transcript naming mikecz De novo discovery 2 12-11-2013 07:49 AM
Using Trinity package aevgup RNA Sequencing 8 02-04-2012 02:15 AM
Trinity assembler error !! empyrean RNA Sequencing 4 12-07-2011 04:38 PM
trinity error ECHo Bioinformatics 3 11-30-2011 12:29 PM
kmer coverage in Trinity Kiroro Bioinformatics 0 09-11-2011 07:24 PM

Thread Tools
Old 04-25-2012, 07:56 AM   #1
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/ 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/ 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/ 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?

jjjscuedu is offline   Reply With Quote
Old 05-07-2012, 02:02 AM   #2
Junior Member
Location: Hartford, CT

Join Date: Sep 2010
Posts: 5
Default compilation errors

Hallo Jingjing!

> /usr/lib64/ 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?
Jackson Laboratory for Genomic Medicine
BenjaminL is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 01:34 PM.

Powered by vBulletin® Version 3.8.6
Copyright ©2000 - 2014, Jelsoft Enterprises Ltd.