David,

I'm cc'ing the galaxy-dev mailing list; let's keep this thread on the list for 
archival and community purposes.

> 
>> I had a look through the Trinity.pl script and found that the default 
>> butterfly 
>> heap is set to 1G.
>> 
>> I've changed this to 2G. Would you re-run the trinity job and let me know if 
>> this helps.

Rather than mucking with the script, It's possible to change the Butterfly 
memory size using command line parameters:

---
Butterfly options:
#
#      --run_butterfly                 :executes butterfly commands.  Do not 
set this if you want to spawn them on a computing grid.
#
#      --bfly_opts                     :parameters to pass through to butterfly 
(see butterfly documentation).
#
#      --bflyHeapSpace                 :java heap space setting for butterfly 
(default: 1000M) => yields command java -Xmx1000M -jar Butterfly.jar ... 
$bfly_opts
---

This can be done in the Trinity wrapper at 
<galaxy-home>/tools/ngs_rna/trinity_all.xml ; there are already some Butterfly 
options set in the wrapper, so it should be easy to add more.

> We see the following at the end of the Trinity logs - I don't know what it 
> means but I thought you might...
> number of good components: 1
> number of reads found = 1253 (from total of 1254) which came from 1252 pairs
> ## Read PathPair results: 1251 singletons,  num pairs: 1, num pairs 
> discarded: 0
> total number of components = 1
> working on subcomponent 0
> method: combineSimilarPathsThatEndAtV(-1) with 1 paths
> method: combineSimilarPathsThatEndAtV(2) with 1 paths
> method: combineSimilarPathsThatEndAtV(1248) with 1 paths
> method: combineSimilarPathsThatEndAtV(1223) with 1 paths
> method: combineSimilarPathsThatEndAtV(-2) with 2 paths
> 
> Path Illustration:
> 
> ====    PATH: [-1, 2, 1248, -2]
> ===     Read: [[-1, 2, 1248], []]   count: 2
>  =      Read: [[2], []]   count: 1030
>  ==     Read: [[2, 1248], []]   count: 23
>  ===    Read: [[2, 1248, -2], []]   count: 2
>   =     Read: [[1248], []]   count: 197
> 
> 
> Final path reported: comp12043_c0_seq1 len=1658 ~FPKM=29.7 path=[2:0-1220 
> 1248:1221-1657]
> FinalPath: [-1, 2, 1248, -2] with support <1254, 1254>
> total number of paths reported = 1 from 1 components
> Done
> SUCCESS[53682]: java -Xmx1G -jar 
> /gpfs/cluster/isys/galaxy/Galaxy/trinityrnaseq_r2011-08-20/Butterfly/Butterfly.jar
>  -N 25506261 -L 300 -F 300 -C chrysalis/RawComps.6/comp12043 -V 10 --stderr
> SUCCESS[53680]: java -Xmx1G -jar 
> /gpfs/cluster/isys/galaxy/Galaxy/trinityrnaseq_r2011-08-20/Butterfly/Butterfly.jar
>  -N 25506261 -L 300 -F 300 -C chrysalis/RawComps.24/comp48425 -V 10 --stderr
> SUCCESS[53681]: java -Xmx1G -jar 
> /gpfs/cluster/isys/galaxy/Galaxy/trinityrnaseq_r2011-08-20/Butterfly/Butterfly.jar
>  -N 25506261 -L 300 -F 300 -C chrysalis/RawComps.8/comp16349 -V 10 --stderr
> 
> 
> Sorry, 1 of 53682 jobs failed.
Overall, this looks very good - almost all the jobs succeeded.
> Failed commands written to file: failed_cmds.27222.txt
> 
> Error, cmd: 
> /gpfs/cluster/isys/galaxy/Galaxy/trinityrnaseq_r2011-08-20/util/cmd_process_forker.pl
>  -c 
> /gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/database/job_working_directory/679/trinity_out_dir/chrysalis/butterfly_commands.adj
>  --CPU 4 --shuffle died with ret 256 at 
> /gpfs/cluster/isys/galaxy/Galaxy/trinityrnaseq_r2011-08-20/Trinity.pl line 
> 571.
This is a bit cryptic to me. You'll want to determine what error code 256 means 
and see whether it may be a memory issue; you may also want to email the 
Trinity mailing list and add for help there.

Good luck,
J.


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