SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
errors running Trinity bioBob Bioinformatics 3 03-30-2013 09:56 PM
Using Trinity package aevgup RNA Sequencing 8 02-04-2012 03:15 AM
Trinity assembler error !! empyrean RNA Sequencing 4 12-07-2011 05:38 PM
Trinity analysis tools tboothby RNA Sequencing 0 11-30-2011 10:59 AM
kmer coverage in Trinity Kiroro Bioinformatics 0 09-11-2011 08:24 PM

Reply
 
Thread Tools
Old 08-29-2011, 08:28 AM   #1
ECHo
Member
 
Location: Taiwan

Join Date: Jan 2010
Posts: 17
Default trinity error

Trinity is the new de novo transcriptome assembly software, and I'm interested in the the software.
According to the manual listed on the website, I tried to test it.
However, there are some errors as follows:
COMMAND: /opt/trinityrnaseq_r2011-08-20/Chrysalis/GraphFromFasta -i inchworm.K25.L48.DS.fa -r both.fa > chrysalis/components.out
Died with exit code 35072
Exiting.
Error, chrysalis did not report butterfly commands file: /data/echo/SRAdb/trinity_out_dir/chrysalis/butterfly_commands at /opt/trinityrnaseq_r2011-08-20/Trinity.pl line 396
main::run_chrysalis('inchworm.K25.L48.DS.fa', 'both.fa', 200, 300, 'undef') called at /opt/trinityrnaseq_r2011-08-20/Trinity.pl line 317
Error, the Chrysalis process failed:
Error, cmd: /opt/trinityrnaseq_r2011-08-20/Chrysalis/Chrysalis -i both.fa -iworm inchworm.K25.L48.DS.fa -o chrysalis -min 200 -dist 300 -butterfly /opt/trinityrnaseq_r2011-08-20/Butterfly/Butterfly.jar died with ret 65280 at /opt/trinityrnaseq_r2011-08-20/Trinity.pl line 571.

In nearly all cases, this is related to not having the stacksize set to unlimited, a prerequisite to running Trinity.
Please visit:

http://trinityrnaseq.sourceforge.net...aq.html#ques_E

for details.

I couldn't understand since my settings for the stack size is unlimited:
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 335872
max locked memory (kbytes, -l) 32
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) unlimited
cpu time (seconds, -t) unlimited
max user processes (-u) 335872
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited

How could I do?
Could somebody give a hint?
Thanks a lot.
ECHo is offline   Reply With Quote
Old 08-30-2011, 02:22 AM   #2
avian
Junior Member
 
Location: Oxford

Join Date: Aug 2011
Posts: 1
Default

You may wish to post this question to the Trinity mailing list for a better explanation of what might have gone wrong, but another common issue relates to the amount of RAM trinity requires. Do you have sufficient resources for the number of reads you are using?
avian is offline   Reply With Quote
Old 11-30-2011, 08:12 AM   #3
tboothby
Member
 
Location: DC

Join Date: May 2011
Posts: 56
Default

I am having a similar problem. My stacksize is set to unlimited. My input is 78M and I have 96G of RAM (Trinity website suggests 1G for every 1M). Has anybody with this problem found a fix?
tboothby is offline   Reply With Quote
Old 11-30-2011, 01:29 PM   #4
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

You could try, as an experiment, running with half of your sequences in order to see if there is a problem with memory or if there is something else wrong.

I agree with the suggestion of sending to the Trinity mailing list. Brian Haas -- one of the Trinity authors -- is very helpful.
westerman is offline   Reply With Quote
Reply

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 07:33 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO