Exception in thread "main" java.io.FileNotFoundException

Question

[croyercolin]

Hi everyone !

I just began in Bioinformatic and I have to deal with my raw data. I want to use Trimmomatic to trim my sequences to 240bp. For that I use this command but I have an error message that I can't solve !

Here it is my code:

java  -jar /Users/myname/Trimmomatic-0.36/trimmomatic-0.36.jar SE 1R1.fastq 1R1CUT.fastq CROP:240

TrimmomaticSE: Started with arguments:

 1R1.fastq 1R1CUT.fastq CROP:240

Automatically using 4 threads

Exception in thread "main" java.io.FileNotFoundException: 1R1.fastq (No such file or directory)

    at java.base/java.io.FileInputStream.open0(Native Method)
    at java.base/java.io.FileInputStream.open(FileInputStream.java:196)
    at java.base/java.io.FileInputStream.<init>(FileInputStream.java:139)
    at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:135)
    at org.usadellab.trimmomatic.TrimmomaticSE.process(TrimmomaticSE.java:197)
    at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:306)
    at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:85)

Do you have any ideas what is going on ? :)

Thank you a lot!

[Joe]

Are you invoking the command from the directory where the fastas are stored? Your error is because Trimmomatic cannot find one or both of your input files.

[croyercolin]

Yes ! Everything are in Trimmomatic-0.36 file where there are the trimmomatic-0.36.jar and my input files with .fastq as extension! :)

[Pierre Lindenbaum]

what is the output of

find /Users/myname/ -type f -name "1R1.fastq" -o -name "1R1CUT.fastq"

?

[croyercolin]

the ouput was :

MacBook-Pro-de-Colin:~ colinroyer$ find /Users/colinroyer/Trimmomatic-0.36/ -type f -name "1R1.fastq" -o -name "1R1CUT.fastq"

/Users/colinroyer/Trimmomatic-0.36//1R1.fastq

:)

[Pierre Lindenbaum]

so where is 1R1CUT.fastq ? what is this double '//' ? It's not a problem with Trimmomatic, it 's a problem with how and where you have generated those fastq files.

[croyercolin]

Well... I want to see my 1R1CUT.fastq. I want to produce this one.

I do not know why I have a double //. It is the answer of the terminal.

I generate my files by copy paste them into the file "Trimmomatic-0.36.jar" I send you a picture of my files composition:

[croyercolin]

Hello ! Thanks for your answers ! The pathway I provide is full and it is the same than the the file trimmomatic-0.36.jar !

The output was :

MacBook-Pro-de-Colin:~ colinroyer$ find /Users/colinroyer/Trimmomatic-0.36/ -type f -name "1R1.fastq" -o -name "1R1CUT.fastq"
/Users/colinroyer/Trimmomatic-0.36//1R1.fastq

So it means it can find my file !

Answer 1

[SaltedPork]

Your error is because Trimmomatic cannot find 1R1.fastq. Try providing the full path to this file and check you've got the file name correct.