Proovread-Teaching: Difference between revisions
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<nowiki>#</nowiki>SBATCH --mail-type=ALL<br> | <nowiki>#</nowiki>SBATCH --mail-type=ALL<br> | ||
<nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u><br> | <nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u><br> | ||
<nowiki>#</nowiki>SBATCH --ntasks=<u> | <nowiki>#</nowiki>SBATCH --ntasks=<u>12</u><br> | ||
<nowiki>#</nowiki>SBATCH --mem=<u>10gb</u><br> | <nowiki>#</nowiki>SBATCH --mem=<u>10gb</u><br> | ||
<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | ||
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cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml proovread/2.14.1-foss-2016b<br> | ml proovread/2.14.1-foss-2016b<br> | ||
proovread -t <u>12</u> <u>[options]</u><br> | |||
</div> | </div> | ||
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values. | In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values. | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml proovread/2.14.1-foss-2016b | ml proovread/2.14.1-foss-2016b | ||
proovread -h | |||
Options: | |||
-l, --long-reads=<FASTA/FASTQ> | |||
PacBio subreads or other erroneous sequences to be corrected. | |||
[-u, --unitigs=<FASTA/FASTQ>] | |||
High confidence unitigs. Can be specified multiple times. | |||
-s, --short-reads=<FASTA/FASTQ> | |||
High confidence short reads. Specify mulitple times for multiple | |||
libs, need to have same format (FASTA/FASTQ and offset 33,64) | |||
-s lib1.fq -s lib2.fq # use reads from two libs | |||
[--sam/--bam=<SAM/BAM>] | |||
External SAM or sorted BAM file instead of --short-reads. | |||
[-p, --prefix=<STRING>] [proovread] | |||
Prefix to output files. | |||
[--overwrite] | |||
Overwrite output folder if it already exists. | |||
[-t, --threads] [4] | |||
Number of threads to use for mapping and consensus. | |||
[--coverage=<INT>] [50] | |||
Estimated short read coverage, 50X recommended. | |||
[-m, --mode] [auto] | |||
Running mode of the pipeline, see README for details. | |||
[--create-cfg=<CFGFILENAME>] [<CWD>/proovread_cfg.pm] | |||
Create a custom config file with advanced options. Does not run the | |||
pipeline. For details, see config header section and README. | |||
[-c, --cfg] | |||
Use custom config file. | |||
[--lr-qv-offset/--sr-qv-offset=<INT>] [auto] | |||
Long/short read quality offset, required if auto-detect fails. | |||
[--ignore-sr-length] | |||
Don't stop if short reads are longer than 700bp. | |||
[--keep-temporary-files] [OFF] | |||
Keep temporary files of each task (BAMs, masked FASTQs, etc.) | |||
[--sample-run] | |||
Run the sample data set to test installation. | |||
[-h, --help] | |||
[-V, --version] | |||
</pre> | </pre> |
Revision as of 15:35, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
2.14.1
Author / Distributor
Description
"PacBio hybrid error correction through iterative short read consensus" More details are at proovread
Running Program
The last version of this application is at /usr/local/apps/eb/proovread/2.14.1-foss-2016b
To use this version, please load the module with
ml proovread/2.14.1-foss-2016b
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_proovread
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=12
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=proovread.%j.out
#SBATCH --error=proovread.%j.err
cd $SLURM_SUBMIT_DIR
ml proovread/2.14.1-foss-2016b
proovread -t 12 [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml proovread/2.14.1-foss-2016b proovread -h Options: -l, --long-reads=<FASTA/FASTQ> PacBio subreads or other erroneous sequences to be corrected. [-u, --unitigs=<FASTA/FASTQ>] High confidence unitigs. Can be specified multiple times. -s, --short-reads=<FASTA/FASTQ> High confidence short reads. Specify mulitple times for multiple libs, need to have same format (FASTA/FASTQ and offset 33,64) -s lib1.fq -s lib2.fq # use reads from two libs [--sam/--bam=<SAM/BAM>] External SAM or sorted BAM file instead of --short-reads. [-p, --prefix=<STRING>] [proovread] Prefix to output files. [--overwrite] Overwrite output folder if it already exists. [-t, --threads] [4] Number of threads to use for mapping and consensus. [--coverage=<INT>] [50] Estimated short read coverage, 50X recommended. [-m, --mode] [auto] Running mode of the pipeline, see README for details. [--create-cfg=<CFGFILENAME>] [<CWD>/proovread_cfg.pm] Create a custom config file with advanced options. Does not run the pipeline. For details, see config header section and README. [-c, --cfg] Use custom config file. [--lr-qv-offset/--sr-qv-offset=<INT>] [auto] Long/short read quality offset, required if auto-detect fails. [--ignore-sr-length] Don't stop if short reads are longer than 700bp. [--keep-temporary-files] [OFF] Keep temporary files of each task (BAMs, masked FASTQs, etc.) [--sample-run] Run the sample data set to test installation. [-h, --help] [-V, --version]
Installation
Source code is obtained from proovread
System
64-bit Linux