Question: Java Exception in Running Trimmomatic software
0
gravatar for modarzi
2.6 years ago by
modarzi140
modarzi140 wrote:

Hi, I have Single End fastq file and it needs trimming. So, I use trimmomatic software for this purpose.based on trimmomatic tutorial I write below code for my .fastq file:

java -jar /home/ubuntu/CIRI_v2.0.6/Trimmomatic-0.36/trimmomatic-0.36.jar SE -threads 2 -phred33 sra_data_SRR1427482.fastq SRR1427482 LEADING:20 TRAILING:20 HEADCROP:14 

TrimmomaticSE: Started with arguments:
 -threads 2 -phred33 sra_data_SRR1427482.fastq SRR1427482 LEADING:20 TRAILING:20 HEADCROP:14

Exception in thread "Thread-0" java.lang.StringIndexOutOfBoundsException: String index out of range: 0
    at java.lang.String.charAt(String.java:658)
    at org.usadellab.trimmomatic.fastq.FastqParser.parseOne(FastqParser.java:65)
    at org.usadellab.trimmomatic.fastq.FastqParser.next(FastqParser.java:179)
    at org.usadellab.trimmomatic.threading.ParserWorker.run(ParserWorker.java:42)
    at java.lang.Thread.run(Thread.java:748)

Input Reads: 47956000 Surviving: 47943826 (99.97%) Dropped: 12174 (0.03%)
TrimmomaticSE: Completed successfully

As you see, my TrimmomaticSE process was completed successfully but during process I phase with exception in java. I need comment for this exception and reason of that. it is important or I can ignore it? Best Regards, Mohammad

rna-seq software error • 927 views
ADD COMMENTlink modified 2.6 years ago by GenoMax93k • written 2.6 years ago by modarzi140
1

Check if you have an empty line at the beginning / end of the file.

ADD REPLYlink written 2.6 years ago by Macspider3.3k
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