<commit_before>#!/bin/bash
#
###############################################################################
#
# "run_deconseq.sh" SuperMikeII script 
# created by <NAME>
# <EMAIL>
# last edited 4 December 2014
#
###############################################################################
#
#PBS -q single
#PBS -A hpc_startup_jelber2
#PBS -l nodes=1:ppn=1
#PBS -l walltime=12:00:00
#PBS -o /work/jelber2/deconseq_ref/
#PBS -j oe
#PBS -N run_deconseq.sh

# Let's mark the time things get started with a date-time stamp.

date

# Set work directory

export WORK_DIR=/work/jelber2/deconseq_ref

# Makes BWA index for the 4 deconseq_ref.fa_c#.fasta files

cd $WORK_DIR
/home/jelber2/bin/deconseq-standalone-0.4.3/perl deconseq.pl -f /work/jelber2/deconseq_ref/SRR649350_1.fastq -dbs deconseq_ref<commit_msg>updated script for 16 cores<commit_after>#!/bin/bash
#
###############################################################################
#
# "run_deconseq.sh" SuperMikeII script 
# created by <NAME>
# <EMAIL>
# last edited 5 December 2014
#
###############################################################################
#
#PBS -q workq
#PBS -A hpc_startup_albuseb
#PBS -l nodes=1:ppn=16
#PBS -l walltime=04:00:00
#PBS -o /work/albuseb/deconseq_out/
#PBS -j oe
#PBS -N run_deconseq.sh

# Let's mark the time things get started with a date-time stamp.

date

# Set work directory

export WORK_DIR=/home/albuseb/bin/deconseq-standalone-0.4.3

# Makes BWA index for the 4 deconseq_ref.fa_c#.fasta files

cd $WORK_DIR
perl /home/albuseb/bin/deconseq-standalone-0.4.3/deconseq_16cores.pl \
-f /work/albuseb/folder_containing_fastq_or_fasta_to_filter/file_to_filter.fastq \
-dbs deconseq_ref \
-out_dir /work/albuseb/deconseq_out
{'fraction_non_alphanumeric': 0.2800925925925926, 'fraction_numerical': 0.03125, 'mean_word_length': 5.356617647058823, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 7, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2681666', 'n_tokens_mistral': 700, 'n_tokens_neox': 625, 'n_words': 139}