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:
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.
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:
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.
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