Dynamic string replacement issue in parallel for repair.sh bbmap

Question

[arunprasanna83]

Hi,

I have many fastq files that I need to repair using repair.sh from bbmap. The filenames are in the format:

AA-60E-76D8.clean.R1.fastq.gz
AA-60E-76D8.clean.R2.fastq.gz

I tried using parallel in the following way as suggested in a previous post.

parallel echo {} {=s/R1/R2/=} ::: *R1.fastq.gz | parallel 'repair.sh in1={} in2={} out1={}.repd.R1.fastq.gz out2={}.repd.R2.fastq.gz outs={}.singletons.fastq.gz repair'

The error I get is the following:

java -ea -Xmx158008m -cp /home/nagaraap/.conda/envs/bbmap/opt/bbmap-38.87-0/current/ jgi.SplitPairsAndSingles rp in1=AA-60E-76D8.clean.R1.fastq.gz AA-60E-76D8.clean.R2.fastq.gz in2=AA-60E-76D8.clean.R1.fastq.gz AA-60E-76D8.clean.R2.fastq.gz out1=AA-60E-76D8.clean.R1.fastq.gz AA-60E-76D8.clean.R2.fastq.gz.repd.R1.fastq.gz out2=AA-60E-76D8.clean.R1.fastq.gz AA-60E-76D8.clean.R2.fastq.gz.repd.R2.fastq.gz outs=AA-60E-76D8.clean.R1.fastq.gz AA-60E-76D8.clean.R2.fastq.gz.singletons.fastq.gz repair

As shown here, the in1 and in2 gets both the values R1, R2 as space separated value. In all the parameters, the sample name is not captured but the entire output of first echo{}.

parallel --version

GNU parallel 20160222

What is the error here?

Thanks in advance.

[cpad0112]

For future reference:

$ ls *.gz
AA-60E-76D8.clean.R1.fastq.gz  AA-60E-76D8.clean.R2.fastq.gz

$ parallel --plus --dry-run 'repair.sh in1={} in2={=s/R1/R2/=} out1={=s/R1/fixed.R1/=} out2={=s/R1/fixed.R2/=} outs={%.R1.fastq.gz}.singletons.fastq.gz repair' ::: *R1.fastq.gz

repair.sh in1=AA-60E-76D8.clean.R1.fastq.gz in2=AA-60E-76D8.clean.R2.fastq.gz out1=AA-60E-76D8.clean.fixed.R1.fastq.gz out2=AA-60E-76D8.clean.fixed.R2.fastq.gz outs=AA-60E-76D8.clean.singletons.fastq.gz repair

[arunprasanna83]

Resolved here. C: How to use BBtools repair.sh on multiple files