Exclude filename in Trimmomatics

Question

[storm1907]

Hello,

I have a problem with BGI RNA-Seq files. When doing Trimmomatics, my script stops exactly at sample 41 in each cell's first lane (V300042149_L01_41_1.fq.gz) in IlluminaClip step. Requesting larger and faster resources from server (more memory, ppn or new nodes with big memory) does not make sense, so I decided just to skip that file.

    #!/bin/bash -x
#PBS -N trimmomatics_job
#PBS -q batch
#PBS -l walltime=72:00:00
#PBS -l feature=summer
#PBS -l feature=largescratch
#PBS -l nodes=wn01:ppn=12;mem=60gb
#PBS -W x=naccesspolicy:UNIQUEUSER
#PBS -j oe
#PBS -A job

INPATH=/dir/dir/dir/subdir/subdir/subdir
OUTPATH=/dir/dir/dir/subdir/subdir/subdir
cd <path to Trimmomatics tool>

shopt -s nullglob

for dir in $INPATH{/,/*/} ;
do
    for file in $dir/*1.fq.gz ;
    do
        bname=$(basename $file '1.fq.gz')
        echo "file: "$file
        echo $bname
        input1=$dir/$bname"1.fq.gz"
        input2=$dir/$bname"2.fq.gz"
        output1=$OUTPATH/$bname"1.paired.fq.gz"
        output2=$OUTPATH/$bname"1.unpaired.fq.gz"
        output3=$OUTPATH/$bname"2.paired.fq.gz"
        output4=$OUTPATH/$bname"2.unpaired.fq.gz"
        echo $input1 $input2
        find . -type f -name V300042149_L01_41_1.fq.gz -prune  -o  -exec trimmomatic-0.39.jar {} \;
        java -jar trimmomatic-0.39.jar PE -threads 4 -phred33 \
            "$input1" "$input2" "$output1" "$output2" "$output3" "$output4" \
            ILLUMINACLIP:BGI_Adapters.fa:2:30:10 \
            LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
    done
done

I have no idea, ho to write this row for excluding the file:

find . -type f -name V300042149_L01_41_1.fq.gz -prune  -o  -exec trimmomatic-0.39.jar {} \;

thank you :)

[Ram]

Nested loops in shell are a bad, bad choice. Surely there must be a better way, maybe create a table of input args first and then run a command per line of that file?

You should use something like find and -not -name "*_41_*" to exclude the 41 files, but definitely look at creating a tabular file with input1, input2, output1, output2, output3, output4 as columns then execute the command per line in that file. You can use the find I suggested while creating this tabular file so the tabular file excludes the 41 files.

Or, your file could just contain the bname values and you could construct everything else on the fly. Just try and get rid of the loop - it is shell abuse.

[Ram]

Oh and by the way, it's trimmomatic, not "trimmomatics".

[Ram]

Another point: You'll almost never need to cd to a tool directory to run it. Only badly built tools work that way. Instead use something like

java -jar /path/to/trimmomatic/trimmomatic-0.39.jar ...

from your working directory so any files dumped in the working directory won't clog up the tool's source directory.