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Old 12-05-2017, 03:07 AM   #1
Batstaph
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Unhappy Trimmomatic adapter file error

I am having a problem getting trimmomatic to find the adapter file. I have tried all the options I can think of for the path, and put the file in the trimmomatic folder but still get a file not found error message. I can't spot any syntax errors, so can anyone help me?

error: java.io.FileNotFoundException: /adapters/Truseq3-PE-2.fa (No such file or directory)


java -jar trimmomatic-0.36.jar PE -phred33 27_4_24_LC_R1.fq 27_4_24_LC_R2.fq 27_4_24_LC_forward_paired.fq 27_4_24_LC_forward_unpaired.fq 27_4_24_LC_reverse_paired.fq 27_4_24_LC_reverse_unpaired.fq ILLUMINACLIP:/adapters/Truseq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Thanks
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Old 12-05-2017, 03:18 AM   #2
GenoMax
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Are you able to list the file by doing an ls with full path?
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Old 12-05-2017, 03:13 PM   #3
neavemj
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I think it searches for that file from your current directory (not from the trimmomatic folder). You could put the adapter file in the same folder as your raw reads, then change that part of your command to the following:

ILLUMINACLIP:Truseq3-PE-2.fa:2:30:10

Cheers,

Matt.
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Old 12-17-2017, 05:19 AM   #4
Batstaph
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Default Now unknown trimmer error

Thanks to both for your responses. Before I had a chance to act I lost access to the computer and only now have new (permanent) machine.
I now have a different issue which is that trimmomatic seems to be identifying my output files as the trimmer and is giving me an 'unknown trimmer' error.

My command line is:
~/Documents/Batstaph/Trimmomatic-0.36$ java -jar trimmomatic-0.36.jar PE -phred33 ~/Documents/Batstaph/sequences/27_4_24_LC R1.fq.gz ~/Documents/Batstaph/sequences/27_4_24_LC R2.fq.gz output_test_FP.fq output_test_RP.fq output_test_FU.fq output_test_RU.fq ILLUMINACLIP:/home/kay/Documents/Batstaph/Trimmomatic-0.36/adapters/Truseq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
and the error message is: Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: test_out_2.paired.fastq
It doesn't seem to matter what I name the output file, trimmomatic is giving me this error at the same point in the command line
Thanks for any tips you can give me.
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Old 12-17-2017, 01:32 PM   #5
mastal
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The error message suggests that you have too many parameters, and trimmomatic is expecting a trimming command at that position, it doesn't really care too much what you call your file. Do you have any unintentional spaces in the names of your files, maybe where the lines wrap in the terminal window, that might make it seem like you had more than just the names of 2 input files and 4 output files?
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Old 12-18-2017, 01:24 AM   #6
Batstaph
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Default Back to old problem

OK, thanks, I removed the spaces in the file names and it has got past the trimmer error. Now I'm back to not finding the adapter file:

java.io.FileNotFoundException: /home/kay/Documents/Batstaph/Trimmomatic-0.36/adapters/Truseq3-PE.fa (No such file or directory)

[email protected]:~/Documents/Batstaph/Trimmomatic-0.36/adapters$ ls
NexteraPE-PE.fa TruSeq2-PE.fa TruSeq2-SE.fa TruSeq3-PE-2.fa TruSeq3-PE.fa TruSeq3-SE.fa

Here is the error and the ls for the path. I can't spot any errors.

Thanks again
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Old 12-18-2017, 02:35 AM   #7
mastal
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What does the ~ expand to on your computer?

If it's something like /users/kay/ instead of /home/kay/
that might explain why you get the directory/file not found error.
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Old 12-18-2017, 03:20 AM   #8
Batstaph
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Pwd gives:

/home/kay/Documents/Batstaph/Trimmomatic-0.36/adapters
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Old 12-18-2017, 06:26 AM   #9
kmcarr
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Quote:
Originally Posted by Batstaph View Post
OK, thanks, I removed the spaces in the file names and it has got past the trimmer error. Now I'm back to not finding the adapter file:

java.io.FileNotFoundException: /home/kay/Documents/Batstaph/Trimmomatic-0.36/adapters/Truseq3-PE.fa (No such file or directory)

[email protected]:~/Documents/Batstaph/Trimmomatic-0.36/adapters$ ls
NexteraPE-PE.fa TruSeq2-PE.fa TruSeq2-SE.fa TruSeq3-PE-2.fa TruSeq3-PE.fa TruSeq3-SE.fa

Here is the error and the ls for the path. I can't spot any errors.

Thanks again
Make the 's' in Truseq uppercase (TruSeq)
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Old 12-18-2017, 08:18 AM   #10
Batstaph
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Default Doh

Stupid error which has been there from the start.

Thank you so much, Trimmomatic worked!!
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