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Unable to access jarfile PE #290
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Hi,
Does setting the env variable TRIMMOMATIC to the trimmomatic jar file solve the issue? Could you also make sure the jar file is executable? |
Thank you for the quick response. TRIMMOMATIC=/scratch/tgeorgom/bulker/bulker_crates/databio/pepatac/1.0.12/trimmomatic and got the same error: > `java -Xmx4000M -jar ${TRIMMOMATIC} PE -threads 1 /scratch/tgeorgom/pepatac_test/test1/fastq/test1_R1.fastq.gz /scratch/tgeorgom/pepatac_test/test1/fastq/test1_R2.fastq.gz /scratch/tgeorgom/pepatac_test/test1/fastq/test1_R1_trim.fastq /scratch/tgeorgom/pepatac_test/test1/fastq/test1_R1_unpaired.fq /scratch/tgeorgom/pepatac_test/test1/fastq/test1_R2_trim.fastq /scratch/tgeorgom/pepatac_test/test1/fastq/test1_R2_unpaired.fq ILLUMINACLIP:/home/tgeorgom/pepatac/tools/NexteraPE-PE.fa:2:30:10` (25453)
<pre>
Error: Unable to access jarfile PE
</pre>
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.031GB.
PID: 25453; Command: java; Return code: 1; Memory used: 0.031GB |
Ok, I see. For a short term solution, you'll need to download the trimmomatic If trimmomatic continues to give you issues, you could also attempt to use skewer. I believe it is faster than trimmomatic. |
I just realized that it's not populating the variable in your second attempt, so the solution above may not work. |
skewer works. |
Yes and I believe it should default to skewer without adjusting the pipeline if not other trimmer is set. Checking the pipeline interface:
From my recent tutorial run using the native install (which defaults to skewer): https://pepatac.databio.org/en/latest/detailed-install/ I see this skewer command from my
Is this helpful? |
Isn't skewer the default trimmer? |
Hi, there,
Could you please help me with this. It seems to be stuck on the trimming level, while calling java?
activated the /scratch/tgeorgom/bulker/bulker_crates/databio/pepatac/1.0.12 image
This is the log file.
for more contex this is my /bulker_config.yaml file
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