Trinity assembler error !!

[empyrean]

Hello all

I ran trinity for RNA Seq data but i am getting the following error.

Error, cmd: /apps/trinityrnaseq_r2011-08-20/Inchworm/bin/inchworm --kmers meryl.kmers.min1.fa --run_inchworm -K 25 -L 48 --monitor 1  --DS  2>monitor.out > inchworm.K25.L48.DS.fa died with ret 256 at /share/apps/trinity/Trinity.pl line 571.

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

   /data//Rnai/transcriptome/assembly/trinity/monitor.out

/share/apps/trinityrnaseq_r2011-08-20/Inchworm/bin/inchworm: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /share/apps/trinityrnaseq_r2011-08-20/Inchworm/bin/inchworm)
/share/apps/trinityrnaseq_r2011-08-20/Inchworm/bin/inchworm: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /share/apps/trinityrnaseq_r2011-08-20/Inchworm/bin/inchworm)

This is for 100 million reads.. when i did the subset and ran for 5 million and 10 million, this is running fine.. Also anything more than 10 million its giving the above error

Also if not this, what assembler could be my next choice? Abyss or Oases or any other transcriptome assemblers??

[saemi]

Hi

How much ram does your computer have? I had problems until I ran it on a server which has about 200 Gb of ram, but I didn't get this error message. I think the Trinity website says you need about 1 Gb of ram per 1 million reads.

My experience is that Trinity seems to do a better job than SOAPdenovo. I haven't tried Abyss or Oases, but people tell my Trinity is better

cheers,Saemi

[empyrean]

i am currently running on a server node which has 256gb ram and 20 processors.

[gringer]

maybe try recompiling on the computer you're running it on? The errors are pointing towards library mismatch problems.

[htchu.taiwan]

Hi, friend,

You may try my program: EBARDenovo for RNA-Seq.

https://sourceforge.net/projects/ebardenovo

It's a 64-bits Windows command with .Net.
You can run 100 million reads on a PC with minimal 16G RAM.
It may take 10 minutes to build indexing information, and 4~6 hours to do assembly.

Remember to use the parameter -T (multithreading) to accelerate the assembly.

Frank H.T. Chu from Taiwan

Hello all

I ran trinity for RNA Seq data but i am getting the following error.

Error, cmd: /apps/trinityrnaseq_r2011-08-20/Inchworm/bin/inchworm --kmers meryl.kmers.min1.fa --run_inchworm -K 25 -L 48 --monitor 1  --DS  2>monitor.out > inchworm.K25.L48.DS.fa died with ret 256 at /share/apps/trinity/Trinity.pl line 571.

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

   /data//Rnai/transcriptome/assembly/trinity/monitor.out

/share/apps/trinityrnaseq_r2011-08-20/Inchworm/bin/inchworm: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /share/apps/trinityrnaseq_r2011-08-20/Inchworm/bin/inchworm)
/share/apps/trinityrnaseq_r2011-08-20/Inchworm/bin/inchworm: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /share/apps/trinityrnaseq_r2011-08-20/Inchworm/bin/inchworm)

This is for 100 million reads.. when i did the subset and ran for 5 million and 10 million, this is running fine.. Also anything more than 10 million its giving the above error

Also if not this, what assembler could be my next choice? Abyss or Oases or any other transcriptome assemblers??