Trinity version: v2.0.6
** NOTE: Latest version of Trinity is v2.1.0, and can be obtained at:
        https://github.com/trinityrnaseq/trinityrnaseq/releases

Paired mode requires bowtie. Found bowtie at: /usr/bin/bowtie

 and bowtie-build at /usr/bin/bowtie-build


-since butterfly will eventually be run, lets test for proper execution of java
Found samtools at: /usr/bin/samtools

#######################################
Running Java Tests
Java tests succeeded.
###################################

Wednesday, October 14, 2015: 13:44:45   CMD: mkdir -p /work/pernaperna/jhonatas/bmc/trinity/trinity_out_dir
CMD finished (0 seconds)
Wednesday, October 14, 2015: 13:44:45   CMD: mkdir -p /work/pernaperna/jhonatas/bmc/trinity/trinity_out_dir/chrysalis
CMD finished (0 seconds)


----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
----------------------------------------------------------------------------------

Converting input files. (in parallel)Wednesday, October 14, 2015: 13:44:45      CMD: /usr/lib/trinityrnaseq/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /work/pernaperna/jhonatas/bmc/trinity/K562_1_paired.fastq >> left.fa 2> /work/pernaperna/jhonatas/bmc/trinity/K562_1_paired.fastq.readcount 
Wednesday, October 14, 2015: 13:44:45   CMD: /usr/lib/trinityrnaseq/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /work/pernaperna/jhonatas/bmc/trinity/K562_2_paired.fastq >> right.fa 2> /work/pernaperna/jhonatas/bmc/trinity/K562_2_paired.fastq.readcount 
CMD finished (70 seconds)
CMD finished (72 seconds)
Wednesday, October 14, 2015: 13:45:57   CMD: cat left.fa right.fa > both.fa
Done converting input files.CMD finished (20 seconds)
-------------------------------------------
----------- Jellyfish  --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------

Wednesday, October 14, 2015: 13:46:18   CMD: /usr/bin/jellyfish count -t 15 -m 25 -s 14446126223  --canonical  both.fa
mkdir: cannot create directory ‘/usr/bin/.libs’: Permission denied
/usr/bin/jellyfish: line 202: cd: /build/jellyfish-sMXWdl/jellyfish-2.2.3: No such file or directory
g++: error: sub_commands/jellyfish.o: No such file or directory
g++: error: sub_commands/count_main.o: No such file or directory
g++: error: sub_commands/info_main.o: No such file or directory
g++: error: sub_commands/dump_main.o: No such file or directory
g++: error: sub_commands/histo_main.o: No such file or directory
g++: error: sub_commands/stats_main.o: No such file or directory
g++: error: sub_commands/merge_main.o: No such file or directory
g++: error: sub_commands/bc_main.o: No such file or directory
g++: error: sub_commands/query_main.o: No such file or directory
g++: error: sub_commands/cite_main.o: No such file or directory
g++: error: sub_commands/mem_main.o: No such file or directory
g++: error: jellyfish/merge_files.o: No such file or directory
g++: error: ./.libs/libjellyfish-2.0.so: No such file or directorynError, cmd: /usr/bin/jellyfish count -t 15 -m 25 -s 14446126223  --canonical  both.fa died with ret 256 at /usr/lib/trinityrnaseq/Trinity line 2115.

Trinity run failed. Must investigate error above.