BLAST+-Teaching: Difference between revisions
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<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | ||
<nowiki>#</nowiki>SBATCH --output=BLAST+.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=BLAST+.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=BLAST+.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml BLAST+/2.6.0-foss-2016b-Python-2.7.14 | ml BLAST+/2.6.0-foss-2016b-Python-2.7.14 | ||
blastn -h | |||
USAGE | USAGE | ||
blastn [-h] [-help] [-import_search_strategy filename] | blastn [-h] [-help] [-import_search_strategy filename] |
Revision as of 14:02, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
2.6.0
Author / Distributor
Description
"Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences." More details are at BLAST+
Running Program
The last version of this application is at /usr/local/apps/eb/BLAST+/2.6.0-foss-2016b-Python-2.7.14
To use this version, please load the module with
ml BLAST+/2.6.0-foss-2016b-Python-2.7.14
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_BLAST+
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=BLAST+.%j.out
#SBATCH --error=BLAST+.%j.err
cd $SLURM_SUBMIT_DIR
ml BLAST+/2.6.0-foss-2016b-Python-2.7.14
blastn [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 BLAST+/2.6.0-foss-2016b-Python-2.7.14 blastn -h USAGE blastn [-h] [-help] [-import_search_strategy filename] [-export_search_strategy filename] [-task task_name] [-db database_name] [-dbsize num_letters] [-gilist filename] [-seqidlist filename] [-negative_gilist filename] [-entrez_query entrez_query] [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm] [-subject subject_input_file] [-subject_loc range] [-query input_file] [-out output_file] [-evalue evalue] [-word_size int_value] [-gapopen open_penalty] [-gapextend extend_penalty] [-perc_identity float_value] [-qcov_hsp_perc float_value] [-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value] [-xdrop_gap_final float_value] [-searchsp int_value] [-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy] [-min_raw_gapped_score int_value] [-template_type type] [-template_length int_value] [-dust DUST_options] [-filtering_db filtering_database] [-window_masker_taxid window_masker_taxid] [-window_masker_db window_masker_db] [-soft_masking soft_masking] [-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value] [-best_hit_score_edge float_value] [-window_size int_value] [-off_diagonal_range int_value] [-use_index boolean] [-index_name string] [-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines] [-outfmt format] [-show_gis] [-num_descriptions int_value] [-num_alignments int_value] [-line_length line_length] [-html] [-max_target_seqs num_sequences] [-num_threads int_value] [-remote] [-version] DESCRIPTION Nucleotide-Nucleotide BLAST 2.6.0+ Use '-help' to print detailed descriptions of command line arguments
Installation
Source code is obtained from BLAST+
System
64-bit Linux