Question: problem with trimmomatic
0
gravatar for mo.ghasemi717
4 months ago by
mo.ghasemi71710 wrote:

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)
rna-seq trimmomatic gene • 231 views
ADD COMMENTlink modified 4 months ago by Lesley Sitter540 • written 4 months ago by mo.ghasemi71710

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

ADD REPLYlink written 4 months ago by Arup Ghosh2.7k

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.

ADD REPLYlink written 4 months ago by WouterDeCoster44k

how can i solve it??

ADD REPLYlink written 4 months ago by mo.ghasemi71710
3
gravatar for Lesley Sitter
4 months ago by
Lesley Sitter540
Netherlands
Lesley Sitter540 wrote:

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

ADD COMMENTlink written 4 months ago by Lesley Sitter540
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1070 users visited in the last hour