bash script loop to join multiple amplicon seq, pair end read on HPC server using ea-utils fastq- join
0
0
Entering edit mode
5.9 years ago
Bioinfonext ▴ 470

Hi,

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:

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

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 • 1.9k views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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?

!/bin/bash 
$ -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

Thanks

ADD REPLY
1
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 1651 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6