d-128-95-149-219:trinityrnaseq_r2012-10-05 sr320$ ./Trinity.pl --seqType fa --JM 20G --single /Users/sr320/Desktop/Olurida_trim_nodups_v2reads.fa
Current settings:
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
file size               (blocks, -f) unlimited
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) unlimited
open files                      (-n) 256
pipe size            (512 bytes, -p) 1
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 709
virtual memory          (kbytes, -v) unlimited


-since butterfly will eventually be run, lets test for proper execution of java
#######################################
Running Java Tests
CMD: java -jar /Users/Shared/Apps/trinityrnaseq_r2012-10-05/util/ExitTester.jar 0
CMD finished (0 seconds)
CMD: java -jar /Users/Shared/Apps/trinityrnaseq_r2012-10-05/util/ExitTester.jar 1
-we properly captured the java failure status, as needed.  Looking good.
Java tests succeeded.
###################################

sh: ldd: command not found
-------------------------------------------
----------- Jellyfish  --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------

CMD: /Users/Shared/Apps/trinityrnaseq_r2012-10-05/trinity-plugins/jellyfish/bin/jellyfish count -t 2 -m 25 -s 873284026  --both-strands  single.fa
Can't exec "/Users/Shared/Apps/trinityrnaseq_r2012-10-05/trinity-plugins/jellyfish/bin/jellyfish": No such file or directory at ./Trinity.pl line 1311.
Error, cmd: /Users/Shared/Apps/trinityrnaseq_r2012-10-05/trinity-plugins/jellyfish/bin/jellyfish count -t 2 -m 25 -s 873284026  --both-strands  single.fa died with ret -1 at ./Trinity.pl line 1315.