Left read files: $VAR1 = [
          '/gscratch/srlab/sr320/data/NR021_R1_comb.fastq'
        ];
Right read files: $VAR1 = [
          '/gscratch/srlab/sr320/data/NR021_R1_comb.fastq'
        ];
Trinity version: Trinity-v2.4.0
-ERROR: couldn't run the network check to confirm latest Trinity software version.

Friday, August 4, 2017: 10:23:32	CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /gscratch/srlab/programs/trinity/util/support_scripts/ExitTester.jar 0
Friday, August 4, 2017: 10:23:33	CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /gscratch/srlab/programs/trinity/util/support_scripts/ExitTester.jar 1


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

---------------------------------------------------------------
------ Quality Trimming Via Trimmomatic  ---------------------
<< ILLUMINACLIP:/gscratch/srlab/programs/trinity/trinity-plugins/Trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 >>
---------------------------------------------------------------


## Running Trimmomatic on read files: /gscratch/srlab/sr320/data/NR021_R1_comb.fastq, /gscratch/srlab/sr320/data/NR021_R1_comb.fastq
Friday, August 4, 2017: 10:23:33	CMD: java -jar /gscratch/srlab/programs/trinity/trinity-plugins/Trimmomatic/trimmomatic.jar PE -threads 50 -phred33  /gscratch/srlab/sr320/data/NR021_R1_comb.fastq /gscratch/srlab/sr320/data/NR021_R1_comb.fastq  NR021_R1_comb.fastq.P.qtrim NR021_R1_comb.fastq.U.qtrim  NR021_R1_comb.fastq.P.qtrim NR021_R1_comb.fastq.U.qtrim  ILLUMINACLIP:/gscratch/srlab/programs/trinity/trinity-plugins/Trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 
TrimmomaticPE: Started with arguments:
 -threads 50 -phred33 /gscratch/srlab/sr320/data/NR021_R1_comb.fastq /gscratch/srlab/sr320/data/NR021_R1_comb.fastq NR021_R1_comb.fastq.P.qtrim NR021_R1_comb.fastq.U.qtrim NR021_R1_comb.fastq.P.qtrim NR021_R1_comb.fastq.U.qtrim ILLUMINACLIP:/gscratch/srlab/programs/trinity/trinity-plugins/Trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Read Pairs: 7613170 Both Surviving: 7613163 (100.00%) Forward Only Surviving: 7 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully
Friday, August 4, 2017: 10:23:48	CMD: cp NR021_R1_comb.fastq.P.qtrim NR021_R1_comb.fastq.PwU.qtrim.fq
Friday, August 4, 2017: 10:23:50	CMD: cp NR021_R1_comb.fastq.P.qtrim NR021_R1_comb.fastq.PwU.qtrim.fq
Friday, August 4, 2017: 10:23:52	CMD: touch trimmomatic.ok
Friday, August 4, 2017: 10:23:52	CMD: gzip NR021_R1_comb.fastq.P.qtrim NR021_R1_comb.fastq.U.qtrim NR021_R1_comb.fastq.P.qtrim NR021_R1_comb.fastq.U.qtrim &
---------------------------------------------------------------
------------ In silico Read Normalization ---------------------
-- (Removing Excess Reads Beyond 50 Coverage --
---------------------------------------------------------------

# running normalization on reads: $VAR1 = [
          [
            'NR021_R1_comb.fastq.PwU.qtrim.fq'
          ],
          [
            'NR021_R1_comb.fastq.PwU.qtrim.fq'
          ]
        ];


Friday, August 4, 2017: 10:23:52	CMD: /gscratch/srlab/programs/trinity/util/insilico_read_normalization.pl --seqType fq --JM 500G  --max_cov 50 --CPU 50 --output /gscratch/srlab/sr320/analyses/trinity_out_dir/insilico_read_normalization   --max_pct_stdev 10000  --left NR021_R1_comb.fastq.PwU.qtrim.fq --right NR021_R1_comb.fastq.PwU.qtrim.fq --pairs_together --PARALLEL_STATS  
Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A /gscratch/srlab/sr320/analyses/trinity_out_dir/NR021_R1_comb.fastq.PwU.qtrim.fq >> left.fa
CMD: seqtk-trinity seq -A /gscratch/srlab/sr320/analyses/trinity_out_dir/NR021_R1_comb.fastq.PwU.qtrim.fq >> right.fa
CMD finished (6 seconds)
CMD finished (6 seconds)
CMD: touch left.fa.ok
CMD finished (0 seconds)
CMD: touch right.fa.ok
CMD finished (0 seconds)
Done converting input files.CMD: cat left.fa right.fa > both.fa
CMD finished (3 seconds)
CMD: touch both.fa.ok
-------------------------------------------
----------- Jellyfish  --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------

CMD finished (0 seconds)
CMD: /gscratch/srlab/programs/trinity/util/..//trinity-plugins/jellyfish/bin/jellyfish count -t 50 -m 25 -s 100000000  --canonical  both.fa
CMD finished (32 seconds)
CMD: /gscratch/srlab/programs/trinity/util/..//trinity-plugins/jellyfish/bin/jellyfish histo -t 50 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
CMD finished (11 seconds)
CMD: /gscratch/srlab/programs/trinity/util/..//trinity-plugins/jellyfish/bin/jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
CMD finished (52 seconds)
CMD: touch jellyfish.K25.min2.kmers.fa.success
CMD finished (0 seconds)
CMD: /gscratch/srlab/programs/trinity/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 50  --DS  > left.fa.K25.stats
CMD: /gscratch/srlab/programs/trinity/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 50  --DS  > right.fa.K25.stats
-reading Kmer occurrences...-reading Kmer occurrences...

gzip: NR021_R1_comb.fastq.P.qtrim: No such file or directory
gzip: NR021_R1_comb.fastq.U.qtrim: No such file or directory

 done parsing 215744308 Kmers, 215744308 added, taking 261 seconds.

 done parsing 215744308 Kmers, 215744308 added, taking 272 seconds.
STATS_GENERATION_TIME: 156 seconds.
slurmstepd: error: *** JOB 54793 ON n2187 CANCELLED AT 2017-08-04T10:32:35 ***