#!/bin/bash
## Job Name
#SBATCH --job-name=Geoduck-trinity-01
## Allocation Definition 
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes (We only get 1, so this is fixed)
#SBATCH --nodes=1   
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=90:30:00
## Memory per node
#SBATCH --mem=500G
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/srlab/sr320/analyses/

 
source /gscratch/srlab/programs/scripts/paths.sh

Trinity \
--seqType fq \
--left /gscratch/srlab/sr320/data/NR021_R1_comb.fastq \
--right /gscratch/srlab/sr320/data/NR021_R1_comb.fastq \
--CPU 50 --trimmomatic --max_memory 500G

[sr320@mox1 analyses]$ squeue | grep srlab
             54793     srlab Geoduck-    sr320  R       8:34      1 n2187
[sr320@mox1 analyses]$ scancel 54793
[sr320@mox1 analyses]$ squeue | grep srlab
[sr320@mox1 analyses]$ 

[sr320@mox1 jobs]$ sbatch -p srlab -A srlab /gscratch/srlab/sr320/jobs/geoduck-trinity-01.sh 
Submitted batch job 54797

Thread 8 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 7 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.