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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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Old 06-01-2014, 01:46 PM   #3
MalcolmHoutz
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Location: Stamford, CT

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Posts: 4
Default Trinity can't find /1 or /2 on many reads

Hi - I am assembling reads using Trinity, which requires a /1 or /2 appended to each left or right hand end of paired reads.
I appended the /1 and /2 using a perl script, checked my work and let it fly. Trinity complains it can't decipher the /1 or /2 on many reads. It prints the read identifier out for the first 10, then gives a count of the total.

I grepped the offending records from both the /1 and /2 fastq's, and they look fine.
Any thoughts?

Here are the warnings from a tiny test run:

CMD: rm bowtie.out
CMD: /share/apps/trinityrnaseq/20131110/Chrysalis//../util/scaffold_iworm_contigs.pl bowtie.nameSorted.sam /scratch/mlh476/rice_project/AZUCENA_trinity_output/inchworm.K25.L25.fa > iworm_scaffolds.txt
warning, ignoring read: HWI-ST911:1412AWEACXX:4:1101:10008:2437 since cannot decipher if /1 or /2 of a pair.
warning, ignoring read: HWI-ST911:1412AWEACXX:4:1101:10030:2102 since cannot decipher if /1 or /2 of a pair.
warning, ignoring read: HWI-ST911:1412AWEACXX:4:1101:10030:2948 since cannot decipher if /1 or /2 of a pair.
warning, ignoring read: HWI-ST911:1412AWEACXX:4:1101:10044:2925 since cannot decipher if /1 or /2 of a pair.
warning, ignoring read: HWI-ST911:1412AWEACXX:4:1101:10044:2925 since cannot decipher if /1 or /2 of a pair.
warning, ignoring read: HWI-ST911:1412AWEACXX:4:1101:10045:2126 since cannot decipher if /1 or /2 of a pair.
warning, ignoring read: HWI-ST911:1412AWEACXX:4:1101:10066:2279 since cannot decipher if /1 or /2 of a pair.
warning, ignoring read: HWI-ST911:1412AWEACXX:4:1101:10071:2111 since cannot decipher if /1 or /2 of a pair.
warning, ignoring read: HWI-ST911:1412AWEACXX:4:1101:10079:2494 since cannot decipher if /1 or /2 of a pair.
warning, ignoring read: HWI-ST911:1412AWEACXX:4:1101:10082:2037 since cannot decipher if /1 or /2 of a pair.
warning, ignoring read: HWI-ST911:1412AWEACXX:4:1101:10082:2037 since cannot decipher if /1 or /2 of a pair.
number of read warnings exceeded 10. Turning off warning messages from here out.
WARNING: note there were 2829 reads that could not be deciphered as being /1 or /2 of a PE fragment. Hopefully, these were SE reads that should have been ignored. Otherwise, please research this further.
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