The bioBakery help forum

Critical error starting trimmomatic (option d64 not recognized)

I’m getting an error from kneaddata (v0.7.10 from conda/biobakery) on the trimmomatic step, the relevant parts of the error message seem to be

CRITICAL ERROR: Error executing: java -Xmx500m -d64 -jar /home/vklepacc/.linuxbrew/bin/trimmomatic-0.33.jar #...
# ...
Error message returned from Trimmomatic :
Unrecognized option: -d64

One bit of weirdness is it’s looking for trimmomatic in linuxbrew folder. When I add trimmomatic with conda (it doesn’t seem to get installed with kneaddata), I get the same error.

$ ls /home/vklepacc/.linuxbrew/bin/trimmomatic-0.33.jar
/home/vklepacc/.linuxbrew/bin/trimmomatic-0.33.jar
$ whereis trimmomatic
trimmomatic: /home/vklepacc/miniconda3/envs/biobakery3/bin/trimmomatic

The former looks like it’s v0.33, while the later is v0.39

$ conda list
# ...
kneaddata                 0.7.10           py37h631d262_0    biobakery
# ...
trimmomatic               0.39                          1    bioconda
full error output
$ kneaddata --input rawfastq/C0932-8F-1A_S44_1.fastq.gz --input rawfastq/C0932-8F-1A_S44_2.fastq.gz --reference-db /nobackup1/vklepacc/databases/Homo_sapiens_bowtie --output output/kneaddata --output-prefix C0932-8F-1A_S44_kneaddata
Decompressing gzipped file ...

Decompressing gzipped file ...

Reformatting file sequence identifiers ...

Reformatting file sequence identifiers ...

Initial number of reads ( /nobackup1b/users/vklepacc/echo/batch014/output/kneaddata/reformatted_identifiersEJ8lab_decompressed_7Qet3C_C0932-8F-1A_S44_1 ): 3737441
Initial number of reads ( /nobackup1b/users/vklepacc/echo/batch014/output/kneaddata/reformatted_identifiersKQ84dB_decompressed_cRnYUK_C0932-8F-1A_S44_2 ): 3737441
Running Trimmomatic ... 
CRITICAL ERROR: Error executing: java -Xmx500m -d64 -jar /home/vklepacc/.linuxbrew/bin/trimmomatic-0.33.jar PE -threads 1 -phred33 /nobackup1b/users/vklepacc/echo/batch014/output/kneaddata/reformatted_identifiersEJ8lab_decompressed_7Qet3C_C0932-8F-1A_S44_1 /nobackup1b/users/vklepacc/echo/batch014/output/kneaddata/reformatted_identifiersKQ84dB_decompressed_cRnYUK_C0932-8F-1A_S44_2 /nobackup1b/users/vklepacc/echo/batch014/output/kneaddata/C0932-8F-1A_S44_kneaddata.trimmed.1.fastq /nobackup1b/users/vklepacc/echo/batch014/output/kneaddata/C0932-8F-1A_S44_kneaddata.trimmed.single.1.fastq /nobackup1b/users/vklepacc/echo/batch014/output/kneaddata/C0932-8F-1A_S44_kneaddata.trimmed.2.fastq /nobackup1b/users/vklepacc/echo/batch014/output/kneaddata/C0932-8F-1A_S44_kneaddata.trimmed.single.2.fastq ILLUMINACLIP:/home/vklepacc/.linuxbrew/lib/python2.7/site-packages/kneaddata/adapters/NexteraPE-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:75

Error message returned from Trimmomatic :
Unrecognized option: -d64
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

I moved the linuxbrew trimmomatic file, but I’m getting the same error pointing to the conda one:

RITICAL ERROR: Error executing: java -Xmx500m -d64 -jar /home/vklepacc/minicond/envs/biobakery3/bin/trimmomatic-0.33.jar 
#...
Error message returned from Trimmomatic :
Unrecognized option: -d64

Hi Kevin - Sorry for the slow response and thank you for the detailed post. I double checked the kneaddata history and we removed the “-d64” option in version v0.7.2. That option is no longer supported with newer versions of java which is where you are seeing the error. Also I think that you might be picking up an older linuxbrew version of kneaddata you have installed instead of the newer conda kneaddata you have installed. If you would remove the whole linuxbrew kneaddata install I think it should resolve the errors.

Thank you,
Lauren

Thanks! That solved this issue, but now having problems with trf :-/

I’ll poke around and open a new thread if I can’t solve. Thanks!