CSAR-web can serve as a convenient and useful scaffolding tool allowing the users to efficiently and accurately scaffold their draft genomes according to a complete or incomplete reference genome. 

Address of the bookmark: http://genome.cs.nthu.edu.tw/CSAR-web

The following table shows SLURM commands on the SOE cluster.

For more information, run man on the commands above. See some examples below.

1. Info about the partitions and nodes
List all the partitions available to you and the nodes therein:

sinfo

Nodes in state idle can accept new jobs.

Show a partition configuratuin, for example, SOE_main

scontrol show partition=SOE_main

Show current info about a specific node:

scontrol show node=<nodename>

You can also specify a group of nodes in the command above. For example, if your MPI job is running across soenode05,06,35,36, you can execute the command below to get the info on the nodes you are interested in:

scontrol show node=soenode[05-06,35-36]

An informative parameter in the output to look at would be CPULoad. It allows you to see how your application utilizes the CPUs on the running nodes.

2. Submit scripts
The header in a submit script specifies job name, partition (queue), time limit, memory allocation, number of nodes, number of cores, and files to collect standard output and error at run time, for example

#!/bin/bash

#SBATCH --job-name=OMP_run     # job name, "OMP_run"
#SBATCH --partition=SOE_main   # partition (queue)
#SBATCH -t 0-2:00              # time limit: (D-HH:MM) 
#SBATCH --mem=32000            # memory per node in MB 
#SBATCH --nodes=1              # number of nodes
#SBATCH --ntasks-per-node=16   # number of cores
#SBATCH --output=slurm.out     # file to collect standard output
#SBATCH --error=slurm.err      # file to collect standard errors

If the time limit is not specified in the submit script, SLURM will assign the default run time, 3 days. This means the job will be terminated by SLURM in 72 hrs. The maximum allowed run time is two weeks, 14-0:00.
If the memory limit is not requested, SLURM will assign the default 16 GB. The maximum allowed memory per node is 128 GB. To see how much RAM per node your job is using, you can run commands sacct or sstat to query MaxRSS for the job on the node - see examples below.
Depending on a type of application you need to run, the submit script may contain commands to create a temporary space on a computational node - see the discussion about using the file systems on the cluster.
Then it sets the environment specific to the application and starts the application on one or multiple nodes - see sbatch sample scripts in directory /usr/local/Samples on soemaster1.hpc.rutgers.edu.
You can submit your job to the cluster with sbatch command:

sbatch myscript.sh

3. Query job information
List all currently submitted jobs in running and pending states for a user:

squeue -u <username>

Command squeue can be run with format options to expose specific information, for example, when pending job #706 is scheduled to start running:

squeue -j 706 --format="%S"

START_TIME
2015-04-30T09:54:32

More info can be shown by placing additional format options, for example:

squeue -j 706 --format="%i %P %j %u %T %l %C %S"

JOBID PARTITION   NAME    USER STATE   TIMELIMIT  CPUS START_TIME
706   SOE_main  Par_job_3 mike PENDING 3-00:00:00 64   2015-04-30T09:54:32

To see when all the jobs, pending in the queue, are scheduled to start:

squeue --start 

List all running and completed jobs for a user

sqlog -u <username>

or

sqlog -j <JobID>

The following appreviations are used for the job states:

       CA   CANCELLED      Job was cancelled.

       CD   COMPLETED      Job completed normally.

       CG   COMPLETING     Job is in the process of completing.

       F    FAILED         Job termined abnormally.

       NF   NODE_FAIL      Job terminated due to node failure.

       PD   PENDING        Job is pending allocation.

       R    RUNNING        Job currently has an allocation.

       S    SUSPENDED      Job is suspended.

       TO   TIMEOUT        Job terminated upon reaching its time limit.

You can specify the fields you would like to see in the output of sqlog:

sqlog --format=list

The command below, for example, provides Job ID, user name, exit state, start date-time, and end date-time for job #2831:

sqlog -j 2831 --format=jid,user,state,start,end

List status info for a currently running job:

sstat -j <jobid>

A formatted output can be used to gain only a specific info, for example, the maximum resident RAM usage on a node:

sstat --format="JobID,MaxRSS" -j <jobid>

To get statistics on completed jobs by jobID:

sacct --format="JobID,JobName,MaxRSS,Elapsed" -j <jobid>

To view the same information for all jobs of a user:

sacct --format="JobID,JobName,MaxRSS,Elapsed" -u <username>

To print a list of fields that can be specified with the --format option:

sacct --helpformat

For example, to get Job ID, Job name, Exit state, start date-time, and end date-time for job #2831:

sacct -j 2831 --format="JobID,JobName,State,Start,End"

Another useful command to gain information about a running job is scontrol:

scontrol show job=<jobid>

4. Cancel a job
To cancel one job:

scancel <jobid>

To cancel one job and delete the TMP directory created by the submit script on a node:

sdel <jobid>

To cancel all the jobs for a user:

scancel -u <username>

To cancel one or more jobs by name:

scancel --name <myJobName>

Structural variants presentation by

Jan Korbel

European Molecular Biology Laboratory (EMBL) Heidelberg Genome Biology Research Unit

Reference: 

https://www.genome.gov/pages/research/der/1000genomesprojecttutorials/structuralvariants-jankorbel.pdf

Address of the bookmark: https://www.nature.com/articles/srep20802

Address of the bookmark: https://sourceforge.net/projects/contiguator/

Address of the bookmark: http://genetics.bwh.harvard.edu/pph2/

• Speed: Prodigal is an extremely fast gene recognition tool (written in very vanilla C). It can analyze an entire microbial genome in 30 seconds or less.
• Accuracy: Prodigal is a highly accurate gene finder. It correctly locates the 3' end of every gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very sophisticated ribosomal binding site scoring system that enables it to locate the translation initiation site with great accuracy (96% of the 5' ends in the Ecogene data set are located correctly).
• Specificity: Prodigal's false positive rate compares favorably with other gene identification programs, and usually falls under 5%.
• GC-Content Indifferent: Prodigal performs well even in high GC genomes, with over a 90% perfect match (5'+3') to the Pseudomonas aeruginosa curated annotations.
• Metagenomic Version: Prodigal can run in metagenomic mode and analyze sequences even when the organism is unknown.
• Ease of Use: Prodigal can be run in one step on a single genomic sequence or on a draft genome containing many sequences. It does not need to be supplied with any knowledge of the organism, as it learns all the properties it needs to on its own.
• Open Source: Prodigal source code is freely available under the General Public License.

Address of the bookmark: http://prodigal.ornl.gov/

Address of the bookmark: http://genomethreader.org/

https://github.com/ewijaya/slidesort-bpr

Address of the bookmark: https://code.google.com/archive/p/slidesort-bpr/

The enzyme portal integrates many resources, most of them hosted by EBI and also external ones such as BioPortal. Its main goal is to provide information about enzymes in a suitable format, with a usable interface designed for intended users. Instead of reinventing the wheel, it makes use of available and reliable resources to that end.

Related Literature:

http://nar.oxfordjournals.org/content/41/D1/D773.full

http://www.biomedcentral.com/1471-2105/14/103

Address of the bookmark: http://www.ebi.ac.uk/enzymeportal/