problem with trimmomatic

Question

[mo.ghasemi717]

hi every one

recently I used trimmomatic for my fastq data but I can't find the output in the current directory where is the problem???

where are they????

my command was:

java -jar trimmomatic-0.39.jar PE ERR3301300_1.fastq ERR3301300_2.fastq ERR3301300_FP.fastq ERR3301300_FU.fastq ERR3301300_RP.fastq ERR3301300_RU.fastq ILLUMINACLIP:adapters/TruSeq3-PE.fa LEADING:1 TRAILING:1

and it showed:

TrimmomaticPE: Started with arguments:
 ERR3301300_1.fastq ERR3301300_2.fastq ERR3301300_FP.fastq ERR3301300_FU.fastq ERR3301300_RP.fastq ERR3301300_RU.fastq ILLUMINACLIP:adapters/TruSeq3-PE.fa LEADING:1 TRAILING:1
Multiple cores found: Using 2 threads
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
    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:8)

[Arup Ghosh]

Make sure the adapter sequence file is properly formatted and present in the location you have mentioned.

[WouterDeCoster]

That's an error. In that case you should not expect to find output, and if you find a file don't trust it. Something went wrong.

[mo.ghasemi717]

how can i solve it??

Answer 1

[Lesley Sitter]

Heya,

Potential reason for this error...

Something could be wrong with your file paths, are you sure all the files are actually in the location from where you are trying to start the tool? It seems the error traces back to the Illumina clipper, so make sure 'adapters/TruSeq3-PE.fa' is the correct path and no typos are made there trimmomatic Errors : "Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1"

Another similar post suggested the supplied adapters in 'adapters/TruSeq3-PE.fa' are too short / incorrectly formatted maybe http://seqanswers.com/forums/archive/index.php/t-20199.html

It seems it's looking for something but cannot find it 'Index 1 out of bounds for length' so i would put my money on the files not being in the place you say they are.. Hope you figure it out :D