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.