Question: bash script loop to join multiple amplicon seq, pair end read on HPC server using ea-utils fastq- join
gravatar for Bioinfonext
21 months ago by
Bioinfonext250 wrote:


I am want to use ea-utils fastq-join to join multiple amplicon sequencing pair end read.

I am working on HPC server but I have installed myself ea-utils as it is not available on server.

so the path for ea-utils is:


and multiple fast files names are like this:

Soil-7_S32_L001_R1_001.fastq.gz   Soil-7_S32_L001_R2_001.fastq.gz
Soil-8_S32_L001_R1_001.fastq.gz  Soil-8_S32_L001_R2_001.fastq.gz
Soil-9_S42_L001_R1_001.fastq.gz  Soil-9_S42_L001_R2_001.fastq.gz

Now, How should I run bash scripts loop to join the multiple files in a single command?

Thanks in advance.

assembly • 832 views
ADD COMMENTlink modified 20 months ago by RamRS30k • written 21 months ago by Bioinfonext250

What have you tried? Or do you just need someone to do all the analysis for you?

ADD REPLYlink written 21 months ago by Benn8.0k

I am trying to use below job scripts but I am not sure If any tool is not available on server then how to load tool in job script which is installed in my own directory, should I use module load or what I have to do exactly?

$ -N fastq-join 
$ -o /users/30521/testdata/test-job 
$ -pe smp-verbose 20
$ /users/30521/testdata/test-job

module load /users/3052/Amplicon_data/ITS_analysis/ITS/ExpressionAnalysis-ea-utils-bd148d4/clipper/fastq-join 

/mnt/scratch/users/staffnumber/ea-utils.1.1.2-537/fastq-join -m 200 -p1 Soil-7_S32_L001_R1_001.fastq Soil-7_S32_L001_R2_001.fastq -o Soil-7_S32_L001.join.fastq
/mnt/scratch/users/staffnumber/ea-utils.1.1.2-537/fastq-join -m 200  -p1 Soil-8_S32_L001_R1_001.fastq Soil-8_S32_L001_R2_001.fastq-o Soil-8_S32_L001_join.fastq
/mnt/scratch/users/staffnumber/ea-utils.1.1.2-537/fastq-join -m 200  -p1 Soil-9_S42_L001_R1_001.fastq Soil-9_S42_L001_R2_001.fastq -o Soil-9_S42_L001_join.fastq


ADD REPLYlink modified 20 months ago by RamRS30k • written 21 months ago by Bioinfonext250

Noone here knows your exact system, but generally using the full path to a software binary which is correctly installed if necessary and visible to all cluster nodes - i.e on a shared storage - should work.

Module load won't help if the software is not installed on your cluster.

Good luck!

ADD REPLYlink written 21 months ago by colindaven2.4k

If fastq-join is located as /users/3052/Amplicon_data/ITS_analysis/ITS/ExpressionAnalysis-ea-utils-bd148d4/clipper/fastq-join, use that location in place of /mnt/scratch/users/staffnumber/ea-utils.1.1.2-537/fastq-join in the last three lines.

If it is located in /mnt/scratch/users/staffnumber/ea-utils.1.1.2-537/fastq-join, remove the module load line.

The concept is well explained by colindaven. module load will only work for modulefiles located in $MODULEPATH, not for custom binaries.

ADD REPLYlink modified 20 months ago • written 20 months ago by RamRS30k
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