Question: Exception in thread "main" java.io.FileNotFoundException
0
gravatar for croyercolin
4 days ago by
croyercolin0 wrote:

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!

sequencing software error • 79 views
ADD COMMENTlink modified 3 days ago • written 4 days ago by croyercolin0

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.

ADD REPLYlink written 4 days ago by jrj.healey3.3k

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

ADD REPLYlink written 4 days ago by croyercolin0

what is the output of

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

?

ADD REPLYlink written 4 days ago by Pierre Lindenbaum104k

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

:)

ADD REPLYlink written 3 days ago by croyercolin0

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.

ADD REPLYlink written 3 days ago by Pierre Lindenbaum104k

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: ScreenPicture of my computer

ADD REPLYlink modified 3 days ago • written 3 days ago by croyercolin0

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 !

ADD REPLYlink modified 3 days ago by Pierre Lindenbaum104k • written 3 days ago by croyercolin0
0
gravatar for SaltedPork
4 days ago by
SaltedPork60
SaltedPork60 wrote:

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.

ADD COMMENTlink written 4 days ago by SaltedPork60
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