The issue is related to illumina clip command.
Error: Exception in thread "main" java.lang.NumberFormatException: For input string: "/Users/Saesha Verma/OneDrive/Desktop/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa"
Code:
java -jar "C:\Users\Saesha Verma\OneDrive\Desktop\Trimmomatic-0.39\trimmomatic-0.39.jar" PE "SRR5337865_1.fastq" "SRR5337865_2.fastq" "Trimmed\out_SRR5337865_1_P.fastq" "Trimmed\out_SRR5337865_1_U.fastq" "Trimmed\out_SRR5337865_2_P.fastq" "Trimmed\out_SRR5337865_2_U.fastq" ILLUMINACLIP:"C:/Users/Saesha Verma/OneDrive/Desktop/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa":2:30:10
Running Trimmomatic directly on Windows, especially older versions like v0.39, can be challenging due to its reliance on Java. Here's how to approach this:
1. Consider alternative tools:
- Trimmomatic online servers: Several online servers offer Trimmomatic functionality. This eliminates the need for local installation and works directly from your web browser. Search for "Trimmomatic online server" to find available options.
- Newer Trimmomatic versions: Explore using newer Trimmomatic versions that might have better Windows compatibility. Newer versions often come with pre-built binaries or offer alternative execution methods. Check the Trimmomatic website (https://github.com/usadellab/Trimmomatic) for download options.
2. If set on using Trimmomatic v0.39 on Windows 11:
- Java installation: Ensure you have Java installed on your system. Download and install the latest Java Runtime Environment (JRE) from the official Oracle website (https://www.oracle.com/java/technologies/downloads/).
- Command Prompt: Navigate to the directory where you have downloaded the Trimmomatic v0.39 JAR file. Open Command Prompt and use the following command format:
java -jar trimmomatic-v0.39.jar
Replace with the specific parameters for your Trimmomatic execution as mentioned in the Trimmomatic documentation (https://github.com/usadellab/Trimmomatic).
Additional Tips:
- Environment variables: Setting environment variables for Java and Trimmomatic might be necessary. Refer to online resources or the Trimmomatic documentation for detailed instructions.
- Community forums: Search online forums and communities dedicated to bioinformatics or Trimmomatic. Users often share solutions and troubleshooting steps for specific issues encountered on Windows.
Important Note: Using an older software version like Trimmomatic v0.39 might not be optimal. Consider exploring alternative tools or using newer Trimmomatic versions for better compatibility and potentially improved functionalities.
If you're encountering issues running Trimmmomatic v0.39 on Windows 11, here are some steps you can take to troubleshoot the problem:
By following these steps, you should be able to troubleshoot and resolve issues with running Trimmmomatic v0.39 on Windows 11. If you continue to encounter difficulties, don't hesitate to seek further assistance from relevant support channels.
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