Trimmomatic error: Exception in thread "main" java.lang.NumberFormatException

Question

[Gilad]

Hello. I tried useing Trimmomatic to trim RNA-seq reads. That is my first time useing it, and my operating system is windows. I'm trying to use the code in cmd just as is presented in the manual, but I'm unable to find solution to my problem.

The script I use is:

java -jar trimmomatic-0.39.jar PE \
  -phred33 \
  C:/Users/yacov/Google_Drive/projects/file_fetch/SRR11813306_1.fastq \
  C:/Users/yacov/Google_Drive/projects/file_fetch/SRR11813306_2.fastq \
  C:/Users/yacov/Google_Drive/projects/file_fetch/SRR11813306_1_paired_trimmed.fastq \
  C:/Users/yacov/Google_Drive/projects/file_fetch/SRR11813306_1_unpaired_trimmed.fastq \
  C:/Users/yacov/Google_Drive/projects/file_fetch/SRR11813306_2_paired_trimmed.fastq \
  C:/Users/yacov/Google_Drive/projects/file_fetch/SRR11813306_2_unpaired_trimmed.fastq \
  ILLUMINACLIP:C:/Users/yacov/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10 \
  LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

I keep getting the same problem:

TrimmomaticPE: Started with arguments:
 -phred33 C:/Users/yacov/Google_Drive/projects/file_fetch/SRR11813306_1.fastq C:/Users/yacov/Google_Drive/projects/file_fetch/SRR11813306_2.fastq C:/Users/yacov/Google_Drive/projects/file_fetch/SRR11813306_1_paired_trimmed.fq.gz C:/Users/yacov/Google_Drive/projects/file_fetch/SRR11813306_1_unpaired_trimmed.fq.gz C:/Users/yacov/Google_Drive/projects/file_fetch/SRR11813306_2_paired_trimmed.fq.gz C:/Users/yacov/Google_Drive/projects/file_fetch/SRR11813306_2_unpaired_trimmed.fq.gz ILLUMINACLIP:C:/Users/yacov/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10:2:True LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Multiple cores found: Using 4 threads
Exception in thread "main" java.lang.NumberFormatException: For input string: "/Users/yacov/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa"
        at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:67)
        at java.base/java.lang.Integer.parseInt(Integer.java:648)
        at java.base/java.lang.Integer.parseInt(Integer.java:778)
        at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:54)
        at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:32)
        at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59)
        at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:552)
        at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)

I tried the fixes I've seen online. Checking for spaces, using full paths. I tried to used different adapters files and I tried to change the created files endings to be fq.gz, nothing solved the problem.

Please help me fix it.

Thank you.

[ATpoint]

Install trimmomatic on windows computer?

Use Linux, please. You're not doing yourself any favor trying to run processing of omics data on a Windows machine.

[pbioinf]

Looks like the argument parser is tripping over the colon after C in the path? Windows woes indeed.

[Gilad]

thank you so much! relative path fixed this specific issu!

[Ram]

Please add an answer and accept it to mark this post as resolved.

[Gilad]

I wish I culd use linux, but I only have my old faithfull laptop that uses windows and no access to a server with linux for example.

[ATpoint]

WSL2 is your friend. It's essentially a seasmless integration of Linux into Windows, developed by Microsoft themselves.