How to run MLST with multiple fastq files

Question

[Kumar]

Hi, I am trying to run a bash script for MLST at CGE (https://cge.cbs.dtu.dk/services/MLST/). I have fastq files and downloaded the MLST program. When I ran the program with single fastq file (R1 and R2) it is able to generate the results but I am getting problem with the batch run in the script. Please see the script below and the error message.

#!/usr/bin/env bash
if [ -z $1 ] ; then
echo "Hint: $0 Input_Directory_Containing_.fastq.gz Speciesname"
exit 1
fi
inputdir=$1
species=$2
export MLST_DB=/home/CGE_server/mlst/mlst_db

cd ~/HOME_MLST
for files in "$inputdir"/*r1.fastq.gz ; do
echo "Working on $files and ${files/r1.fastq.gz/r2.fastq.gz} for species $species"
#cp $files ${files/r1.fastq.gz/r2.fastq.gz} .
bfile=$(basename $files)
mkdir "${bfile%%r1.fastq.gz}"
sudo docker run --rm -it -v $MLST_DB:/database -v $(pwd):/workdir mlst -i $bfile ${bfile/r1.fastq.gz/r2.fastq.gz} -o ${bfile%%r1.fastq.gz} -s $species -x
echo "Finished working on $files"
done

ERROR:

$bash mlst.sh ecoli
Working on ecoli/*r1.fastq.gz and ecoli/*r2.fastq.gz for species 
usage: mlst.py [-h] -i INFILE [INFILE ...] [-o OUTDIR] -s SPECIES
           [-p DATABASE] [-t TMP_DIR] [-mp METHOD_PATH] [-x] [-q]
           [-matrix]
mlst.py: error: argument -s/--species: expected one argument
Finished working on ecoli/*r1.fastq.gz

Answer 1

[cfos4698]

Your script isn't doing what you intend it to do, or, at least, you aren't running it in a way that makes it work as intended. Your script expects the first command line arg to be the inputdir, and the second command line arg to be the species name. However, you're running it this way:

bash mlst.sh ecoli

So, 'ecoli' is treated as the inputdir, and no species name is provided. Hence, the second command arg ($2) is empty, which leads to the 'species' variable being empty, and the -s flag of mlst.py evaluates to nothing. Accordingly, the following error occurs: 'error: argument -s/--species: expected one argument'.

Try the following:

#!/usr/bin/env bash
[ "$#" -ne 2 ] &&  echo "Hint: $0 Input_Directory_Containing_.fastq.gz Speciesname" && exit 1

inputdir=$1
species=$2
export MLST_DB=/home/CGE_server/mlst/mlst_db

cd ~/HOME_MLST

for i in "${inputdir}"/*.r1.fastq.gz ; do
R1=${i}
R2=${i/.r1.fastq.gz/.r2.fastq.gz}
echo $R1
echo $R2
outname=${R1%.r1.fastq.gz}
mkdir ${outname}

echo "Working on ${R1} and ${R2} for species $species"

sudo docker run --rm -it -v $MLST_DB:/database -v $(pwd):/workdir mlst -i ${R1} ${R2} -o ${outname} -s ${species} -x
echo "Finished working on ${outname}"
done

Note: I can't run the program, so just assuming this will work.

[Kumar]

Hi, Thank you for your suggestions.

I am running the script. However, it shows below error.

 $bash mlst.sh ecoli

error message:

Hint: mlst.sh Input_Directory_Containing_.fastq.gz Speciesname

[cfos4698]

Did you try thinking about what to do after seeing the hint and seeing the long answer I wrote? I specifically said "Your script expects the first command line arg to be the inputdir, and the second command line arg to be the species name." You only provided one command line argument, the species name, and it was in the wrong position. What's missing? What order should you put the arguments in?

[Kumar]

Off course. I read your comments otherwise how I knew the error. As script expects the first command line arg to be the inputdir, and the second command line arg to be the species name, I am giving first argument mlst.sh and second ecoli.

Anyway I ran my script with the same running command ($bash mlst.sh ecoli) as inputdir (pwd) and got run.

inputdir=$(pwd) species=$1

[cfos4698]

You ran bash mlst.sh species.

mlst.sh is a file, not a directory.

Correct:

bash mlst.sh inputdir species

[Kumar]

Thank you for letting me know. I tried in this way also but it show following error. I am in working directory and giving the command (bash mlst.sh /home/MLST/ ecoli). Sorry I am new in bash scripting.

/home/MLST//*.r1.fastq.gz
/home/MLST//*.r2.fastq.gz
mkdir: cannot create directory ‘/home/MLST//Lm03_S7_L001_r1.fastq.gz’: File exists
mkdir: cannot create directory ‘/home/MLST//Lm03_S7_L001_r2.fastq.gz’: File exists
mkdir: cannot create directory ‘/home/MLST//mlst_full_directoryfastq.sh’: File exists
mkdir: cannot create directory ‘/home/MLST//mlst.sh’: File exists
Working on /home/MLST//*.r1.fastq.gz and /home/bmaurice/LM_MLST//*.r2.fastq.gz for species ecoli
usage: mlst.py [-h] -i INFILE [INFILE ...] [-o OUTDIR] -s SPECIES
           [-p DATABASE] [-t TMP_DIR] [-mp METHOD_PATH] [-x] [-q]
           [-matrix]
 mlst.py: error: unrecognized arguments: /home/MLST//Lm03_S7_L001_r2.fastq.gz /home/MLST//mlst_full_directoryfastq.sh /home/MLST//mlst.sh
 Finished working on /home/MLST//*