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Using trimmomatic on multiple paired-end read files

I need help to write a for loop to run Trimmomatic tool for quality trimming of paired end fastq files. I need to write a for loop so that I can run an executable for all multiple files.

Input PE files looks like - C1_R1.fastq

C1_R2.fastq

C2_R1.fastq

C2_R2.fastq

C3_R1.fastq

C3_R2.fastq

T1_R1.fastq

T1_R2.fastq

T2_R1.fastq

T2_R2.fastq

T3_R1.fastq

T3_R2.fastq

To run trimmomatic for the paired reads corresponding to C1_R1.fastq and C1_R2.fastq, the following command works:

java -jar ~/Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 C1_R1.fastq C1_R2.fastq C1_R1_paired.fastq C1_R1_unpaired.fastq C1_R2_paired.fastq C1_R2_unpaired.fastq LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35

I have tried using this thread, but I am unable to understand.

Any help please! Thanks!

ngs assembly genome next-gen sequencing
• 16,462 views • link
updated by lakhujanivijay lakhujanivijay • written by bioinformaticssrm2011 bioinformaticssrm2011

Hi bioinformaticssrm2011,

The second command I posted on seqanswers (with an echo in front) should show you the command how it would be executed. That way you can figure out what is wrong.

Shouldn't you use this command in paired end mode?

java -jar <path to trimmomatic.jar> PE [-threads <threads] [-phred33 | -phred64] [-trimlog <logFile>] >] [-basein inputBase> | <input 1> <input 2>] [-baseout <outputBase> | <unpaired output 1> <paired output 2> <unpaired output 2> <step 1> ...
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written by WouterDeCoster WouterDeCoster

I've seen that error. Now read what I wrote about using the echo statement and figuring out what's wrong.

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written by WouterDeCoster WouterDeCoster

About echo, I am new to this, so unable to understand it. Sorry

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written by bioinformaticssrm2011 bioinformaticssrm2011

If you don't know the echo command you need to start with following a command line tutorial, that will make everything less painful.

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written by WouterDeCoster WouterDeCoster

this is my python script 

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import subprocess

with open('/data2/masw_data/Nanda/5A_and_5D/bbmap_config.txt', 'r') as f:
    for line in f:
        line = line.strip().split()
        ref, in1, in2, outm = line
        proc = subprocess.Popen(['/data1/masw/bbmap/bbmap.sh', ref, in1, in2, outm, 'threads=20', 'minid=0.70', 'nodisk'], shell=False)
        proc.wait()
f.writelines()
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updated by GenoMax GenoMax • written by shengweima • shengweima

shengweima : Did you post in the wrong thread or were you presenting an example?

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written by GenoMax GenoMax

2 answers

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written by lakhujanivijay lakhujanivijay

You need to specify the directories to your input/output files :

"inputdirectory" directory "processed" directory (as output) "log" directory for log information "program" directory with Trimmomatic jar file

#! python
import os
import sys
import subprocess 

for fileR1 in os.listdir(inputdirectory): 
    dividing = fileR1.split(".")
    if ("R1" in fileR1) :
        fileR2 = fileR1.replace('R1', 'R2')
        if os.path.isfile(inputdirectory + fileR2) :
            dividing1 = fileR2.split(".")
            log1 = dividing[0]
            output1 = dividing[0]
            output2 = dividing1[0]
            subprocess.call("java -jar " + program + "trimmomatic-0.35.jar PE -threads 12 -phred33 " + inputdirectory + fileR1 + " " + inputdirectory + fileR2 + " " + processed + output1 +"_trimmed.fastq.gz " +  "output_forward_unpaired.fq.gz "  + processed + output2 + "_trimmed.fastq.gz " + "output_reverse_unpaired.fq.gz " + " LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35" +" >" + log + log1 + "_trimmomatic.txt" + " 2>&1", shell=True)

Hope it helps :) Best,

Agata

• 0 views • link
written by agata88 agata88

Hi, thanks for your help. But I got an error

File "python.py", line 8 if ("R1" in fileR1): ^ IndentationError: unindent does not match any outer indentation level

than I checked the indent and tried to solve it, and later I got another error-

Traceback (most recent call last): File "python.py", line 6, in <module> for fileR1 in os.listdir(input): TypeError: coercing to Unicode: need string or buffer, builtin_function_or_method found

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written by bioinformaticssrm2011 bioinformaticssrm2011

input shouldn't be used as a variable name in python3. Make it inputfile or something like that.

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written by WouterDeCoster WouterDeCoster

Thats helpful.

but another error pop up-

Traceback (most recent call last): File "python.py", line 6, in <module> for fileR1 in os.listdir(inputfile): NameError: name 'inputfile' is not defined

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written by bioinformaticssrm2011 bioinformaticssrm2011

That's because you didn't define the variable.

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written by WouterDeCoster WouterDeCoster

Yes, that is correct it shouldn’t be 'input' , I forgot about that when I was changing names... sorry ... going to change that right now.

• 0 views • link
written by agata88 agata88

Changed, now it should be ok, also the indentation was repaired.

• 0 views • link
written by agata88 agata88

hi, When I was trying to use above script, I got an error.

    #! python
    import os
    import sys
    import subprocess 
    inputdirectory = "/home/shashank/Desktop/patel_chest_NSC/inputdirectory"
   processed = "/home/shashank/Desktop/patel_chest_NSC/processed"
   log="/home/shashank/Desktop/patel_chest_NSC/log"
   for fileR1 in os.listdir(inputdirectory): 
        dividing = fileR1.split(".")
        if ("R1" in fileR1) :
            fileR2 = fileR1.replace('R1', 'R2')
            if os.path.isfile(inputdirectory + plikR2) :
                dividing1 = fileR2.split(".")
                log1 = dividing[0]
                output1 = dividing[0]
                output2 = dividing1[0]
                subprocess.call("java -jar " + program + "~/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads 12 -phred33 " + inputdirectory + fileR1 + " " + inputdirectory + fileR2 + " " + processed + output1 +"_trimmed.fastq.gz " +  "output_forward_unpaired.fq.gz "  + processed + output2 + "_trimmed.fastq.gz " + "output_reverse_unpaired.fq.gz " + " LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35" +" >" + log + log1 + "_trimmomatic.txt" + " 2>&1", shell=True)

Error is- 

   Traceback (most recent call last):
  File "python.py", line 10, in <module>
    if os.path.isfile(inputdirectory + plikR2) :
NameError: name 'plikR2' is not defined
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written by bioinformaticssrm2011 bioinformaticssrm2011

Please replace 'plikR2' to 'fileR2'.

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written by agata88 agata88

Hi, Thanks for you python script. I am trying to run this script but I have it not running or giving me any output. and also, I have no error come at any step. when I run it the result is nothing. Can you help me, please! Thanks

• 0 views • link
written by Safa.A • Safa.A

Hi, check the indentations. maybe during copy/paste something was shifted, best, Agata

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written by agata88 agata88

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