Trimmomatic error while executing

[Irina Pulyakhina]

Hi everyone,

I'm trying to run Trimmomatic v0.15. I'm working with Illumina paired end data. With this command:

java -classpath ./trimmomatic.jar org.usadellab.trimmomatic.TrimmomaticSE initial_test_set1 out_file ILLUMINACLIP:illuminaClipping.fa:2:40:15 MINLEN:36

(all file for sure exist in the corresponding folders)
I get the following error:
=========================
Exception in thread "main" java.lang.NoClassDefFoundError: org/usadellab/trimmomatic/TrimmomaticSE
Caused by: java.lang.ClassNotFoundException: org.usadellab.trimmomatic.TrimmomaticSE
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
Could not find the main class: org.usadellab.trimmomatic.TrimmomaticSE. Program will exit.
=========================

Does anyone now how to solve it?

Thanks in advance,
Irina

[westerman]

Probably means that ./trimmomatic.jar does not exist.

[giorgifm]

Dear Irina,

first of all, thanks for using Trimmomatic :-)

Try substituting in your command line ./trimmomatic.jar with trimmomatic-0.15.jar (the jar file name) or the jar name of the version you are using.

[ssing]

I think I found a small hiccup in Trimmomatic (easily fixed by the user, but it might be good to clarify somewhere on the website) -- when providing sequences for the adapters, the file has to be in the directory where Trimmomatic is. It would be nice if this could be flexible and the sequences could be anywhere.

Great program and excellent documentation -- thanks!

[kga1978]

when providing sequences for the adapters, the file has to be in the directory where Trimmomatic is.

Not so. You can specify this with the following: ILLUMINACLIP:<path to contaminants.fasta>:X:X:X

One small mistake I have found though is that "MINLEN" is specified as "MINLENGTH" in the documentation - the latter doesn't work.

[morning latte]

Trimmomatic error

Hi,
I have had no problem running Trimmomatic so far with Illumina HiSeq fastq files provided by sequencing core. However, Trimmomatic started generating output files that contain nothing. The difference from the previous run and this run is that I trimmed some of reads at their 5' ends using HOMER and I assume that HOMER output format (which still looks fastq files for me) causes a problem on Trimmomatic. I tried with -phred33 and -phred64 but nothing worked. Do you have any suggestions? Thanks.

[Hparker]

I am also having a similar problem with trimmomatic version 0.33:

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Exception in thread "main" java.lang.NoClassDefFoundError: org/usadellab/trimmomatic/TrimmomaticPE
Caused by: java.lang.ClassNotFoundException: org.usadellab.trimmomatic.TrimmomaticPE
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
Could not find the main class: org.usadellab.trimmomatic.TrimmomaticPE. Program will exit.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Is anyone able to help?

Many thanks.

[GenoMax]

I am also having a similar problem with trimmomatic version 0.33:

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Exception in thread "main" java.lang.NoClassDefFoundError: org/usadellab/trimmomatic/TrimmomaticPE
Caused by: java.lang.ClassNotFoundException: org.usadellab.trimmomatic.TrimmomaticPE
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
Could not find the main class: org.usadellab.trimmomatic.TrimmomaticPE. Program will exit.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Is anyone able to help?

Many thanks.

Post the complete command you are using.

[Hparker]

command I am using:

$ java -Xmx2G -classpath trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE in291_1_s1_R1.fastq.gz in291_1_s1_R2.fastq.gz in291_1_s1_R1.paired.fastq.gz in291_1_s1_R1.single.fastq.gz in291_1_s1_R2.paired.fastq.gz n291_1_s1_R2.single.fastq.gz LEADING:20 TRAILING:20

[GenoMax]

command I am using:

$ java -Xmx2G -classpath trimmomatic-0.33.jar org.usadellab.trimmomatic.TrimmomaticPE in291_1_s1_R1.fastq.gz in291_1_s1_R2.fastq.gz in291_1_s1_R1.paired.fastq.gz in291_1_s1_R1.single.fastq.gz in291_1_s1_R2.paired.fastq.gz n291_1_s1_R2.single.fastq.gz LEADING:20 TRAILING:20

Try this (replace path_to with real path, I assume you have sanger fastq format files).

$ java -jar [COLOR="Red"]/path_to/[/COLOR]trimmomatic-0.33.jar PE -phred33 in291_1_s1_R1.fastq.gz in291_1_s1_R2.fastq.gz in291_1_s1_R1.paired.fastq.gz in291_1_s1_R1.single.fastq.gz in291_1_s1_R2.paired.fastq.gz n291_1_s1_R2.single.fastq.gz LEADING:20 TRAILING:20

[Hparker]

Using the full path also does not work...

[yueluo]

What files/directories do you have in your trimmomatic path? You might be missing some files.

[Hparker]

In the path to the trimmomatic I have the following files:

fastq files
trimmomatic-0.33.jar file
adapters folder from trimmomatic zip
LICENSE file from trimmomatic zip

[hoppo]

When you move into the directory where the trimmomatic jar is located and execute:-

java -jar trimmomatic-0.33.jar

Do you get any output (or the same error)?

Also, the last paramerer is.. n291_1_s1_R2.single.fastq.gz
Is this correct? or should it be in291_1_s1_R2.single.fastq.gz

[Hparker]

I get the info on how to use it:

Usage:
PE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
or:
SE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] <inputFile> <outputFile> <trimmer1>...

I have now changed the in code I use to:

java -jar /home/Shared/data/seq/hannah_Zymo_June2015/FASTQ/trimmomatic-0.33.jar PE in291_10_s1_R1.fastq.gz in291_10_s1_R2.fastq.gz in291_10_s1_R1.paired.fastq.gz in291_10_s1_R1.single.fastq.gz in291_10_s1_R2.paired.fastq.gz in291_10_s1_R2.single.fastq.gz LEADING:20 TRAILING:20

..and this seems to be working- I get something like this:

Multiple cores found: Using 16 threads
Quality encoding detected as phred33
Input Read Pairs: 221445 Both Surviving: 221445 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully

I hope this is correct! It only takes a few seconds for it to do the trimming..

What is the difference with using -Xmx2G and not specifying this?