200+ samples to run with SSPACE

Question

[tpaisie]

I have around 270 samples of Salmonella. I'm trying to use the program SSPACE to extend and scaffold pre-assembled contigs. Here is my set up of the library.txt file (with less samples):

SRR1122483 bowtie SRR1122483_pair_1.fastq SRR1122483_pair_2.fastq 200 0.75 FR
SRR1122484 bowtie SRR1122484_pair_1.fastq SRR1122484_pair_2.fastq 200 0.75 FR
SRR1122485 bowtie SRR1122485_pair_1.fastq SRR1122485_pair_2.fastq 200 0.75 FR
SRR1122486 bowtie SRR1122486_pair_1.fastq SRR1122486_pair_2.fastq 200 0.75 FR
SRR1122487 bowtie SRR1122487_pair_1.fastq SRR1122487_pair_2.fastq 200 0.75 FR

And here is my command for SSPACE:

DIR=$1
SSPACE.pl -l library.txt -s spades_output/${DIR}/contigs.fasta -x 1 -m 32 -o 20 -k 5 -a 0.70 -n 15 -p 0 -v 1 -z 200 -g 0 -T 6 -b ${DIR}

If anyone could help me find a way where I can run SSPACE on all the samples in my library.txt file without having to enter each sample separately it would be greatly appreciated. Thanks!!!

[Pierre Lindenbaum]

do you mean you want to build the file library.txt from a directory of fastq files ?

[tpaisie]

So I have my library.txt file already made with all the samples I want to run included in it, but I am unable to run all these samples at the same time or even sequentially. I have been having to do run this program one sample at a time. For example, I have to change my library.txt file to:

SRR1292311 bowtie SRR1292311_pair_1.fastq SRR1292311_pair_2.fastq 200 0.75 FR

When I try to run SSPACE with more than one sample in the library.txt file, it will not run. For example a library.txt that looks like this:

SRR1292311 bowtie SRR1292311_pair_1.fastq SRR1292311_pair_2.fastq 200 0.75 FR
SRR1299291 bowtie SRR1299291_pair_1.fastq SRR1299291_pair_2.fastq 200 0.75 FR

I cannot get the program to run on both samples.

[fabiomarcelomedvet]

Hi tpaisie. Have you tried a bash script?

!/bin/bash

Immediately stop on errors. keep track of the commands as they get executed.

set -uex shopt -s extglob

Samples list.

array=( "SRR1299291" "SRR1292311" )

for i in ${array[@]} do ./SSPACE_Standard_v3.0.pl -l "$i"library.txt -s "$i"fasta_file -k 5 -a 0.7 \ -x 0 -b "$i"output_name

done