Left read files: $VAR1 = [
          '/gscratch/srlab/sr320/data/NR021_R1_comb.fastq'
        ];
Right read files: $VAR1 = [
          '/gscratch/srlab/sr320/data/NR021_R2_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: 10:48:33	CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /gscratch/srlab/programs/trinity/util/support_scripts/ExitTester.jar 0
Friday, August 4, 2017: 10:48:33	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_R2_comb.fastq
###############################################################################
#### Trimmomatic  process was previously completed. Skipping it and using existing qual-trimmed files: NR021_R1_comb.fastq.PwU.qtrim.fq, NR021_R2_comb.fastq.PwU.qtrim.fq
###############################################################################
---------------------------------------------------------------
------------ In silico Read Normalization ---------------------
-- (Removing Excess Reads Beyond 50 Coverage --
---------------------------------------------------------------

# running normalization on reads: $VAR1 = [
          [
            'NR021_R1_comb.fastq.PwU.qtrim.fq'
          ],
          [
            'NR021_R2_comb.fastq.PwU.qtrim.fq'
          ]
        ];


Friday, August 4, 2017: 10:48:34	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_R2_comb.fastq.PwU.qtrim.fq --pairs_together --PARALLEL_STATS  
Converting input files. (both directions in parallel)left file exists, nothing to doright file exists, nothing to do-------------------------------------------
----------- Jellyfish  --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------

-sorting each stats file by read name.
Done converting input files.Thread 4 terminated abnormally: Error, not all specified records have been retrieved (missing 907086) from /gscratch/srlab/sr320/analyses/trinity_out_dir/NR021_R2_comb.fastq.PwU.qtrim.fq, see file: /gscratch/srlab/sr320/analyses/trinity_out_dir/insilico_read_normalization/NR021_R2_comb.fastq.PwU.qtrim.fq.normalized_K25_C50_pctSD10000.fq.missing_accs for list of missing entries at /gscratch/srlab/programs/trinity/util/insilico_read_normalization.pl line 548.
Thread 3 terminated abnormally: Error, not all specified records have been retrieved (missing 907086) from /gscratch/srlab/sr320/analyses/trinity_out_dir/NR021_R1_comb.fastq.PwU.qtrim.fq, see file: /gscratch/srlab/sr320/analyses/trinity_out_dir/insilico_read_normalization/NR021_R1_comb.fastq.PwU.qtrim.fq.normalized_K25_C50_pctSD10000.fq.missing_accs for list of missing entries at /gscratch/srlab/programs/trinity/util/insilico_read_normalization.pl line 548.
Error encountered with thread.
Error encountered with thread.
Error, at least one thread died at /gscratch/srlab/programs/trinity/util/insilico_read_normalization.pl line 419.
Error, 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_R2_comb.fastq.PwU.qtrim.fq --pairs_together --PARALLEL_STATS   died with ret 6400 at /gscratch/srlab/programs/trinity/Trinity line 2462.