Salmonid Trinity Run

Since file transfers to/from Hyak are being wonky and I already have the files uploaded, I’m going to start Andrew Spanjer’s salmon trinity assembly.

First, I need to make a new BlastX database using files provided by Andrew.

/gscratch/srlab/programs/ncbi-blast-2.6.0+/bin/makeblastdb  -in SalmonUni.fasta -parse_seqids -dbtype prot

Building a new DB, current time: 05/12/2017 09:26:38
New DB name:   /gscratch/srlab/data/andrew-trinity/SalmonUni.fasta
New DB title:  SalmonUni.fasta
Sequence type: Protein
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 141125 sequences in 5.81965 seconds.

Andrew supplied me with his two data files, all_val_1.fq.gz and all_val_2.fq.gz, so I threw those in to a slum batch file and fired up trinity via slurs..

[seanb80@mox1 andrew-trinity]$ cat TrinRun.sh 
#!/bin/bash
## Job Name
#SBATCH --job-name=Salmon_Trinity
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (ten minutes)
#SBATCH --time=480:00:00
## Memory per node
#SBATCH --mem=350G
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/srlab/data/andrew-trinity/

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

Trinity --seqType fq --left all_val_1.fq.gz --right all_val_2.fq.gz  --CPU 50 --trimmomatic --max_memory 350G

[seanb80@mox1 andrew-trinity]$ sbatch -p srlab -A srlab TrinRun.sh
Submitted batch job 13312
[seanb80@mox1 andrew-trinity]$ scontrol show job 13312
JobId=13312 JobName=Salmon_Trinity
   UserId=seanb80(557445) GroupId=hyak-srlab(415510) MCS_label=N/A
   Priority=276 Nice=0 Account=srlab QOS=normal
   JobState=RUNNING Reason=None Dependency=(null)
   Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0
   RunTime=00:00:04 TimeLimit=20-00:00:00 TimeMin=N/A
   SubmitTime=2017-05-12T09:56:15 EligibleTime=2017-05-12T09:56:15
   StartTime=2017-05-12T09:56:17 EndTime=2017-06-01T09:56:17 Deadline=N/A
   PreemptTime=None SuspendTime=None SecsPreSuspend=0
   Partition=srlab AllocNode:Sid=mox1:38936
   ReqNodeList=(null) ExcNodeList=(null)
   NodeList=n2203
   BatchHost=n2203
   NumNodes=1 NumCPUs=28 NumTasks=1 CPUs/Task=1 ReqB:S:C:T=0:0:*:*
   TRES=cpu=28,mem=350G,node=1
   Socks/Node=* NtasksPerN:B:S:C=0:0:*:* CoreSpec=*
   MinCPUsNode=1 MinMemoryNode=350G MinTmpDiskNode=0
   Features=(null) DelayBoot=00:00:00
   Gres=(null) Reservation=(null)
   OverSubscribe=NO Contiguous=0 Licenses=(null) Network=(null)
   Command=/gscratch/srlab/data/andrew-trinity/TrinRun.sh
   WorkDir=/gscratch/srlab/data/andrew-trinity/
   StdErr=/gscratch/srlab/data/andrew-trinity//slurm-13312.out
   StdIn=/dev/null
   StdOut=/gscratch/srlab/data/andrew-trinity//slurm-13312.out
   Power=

Watching top in another window, everything seems to be running ok, but trimmomatic seems to only be using ~ 8 cores, hopefully trinity will be better

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#sbatch