Open sunta3iouxos opened 2 weeks ago
Hi,
java -Xmx4000M -jar ${TRIMMOMATIC} PE
may offer some clues.
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.
After activating the pepatak environment and looking for echo ${TRIMMOMATIC}
I get empty response. Maybe it is not properly set in the bulker?
Anyway this is what I did:
activated the environmet
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 jar
file and set your environment variable to the location of the jar
file. Not the directory within the bulker crate like you have above. Apologies that this is confusing.
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. Could you please state the options you are using for skewer? I had some issues with skewer in the past and had to do with quality trimming and a couple of other things. Overall, was not that reliable, although very fast. I use fastp without issues, with those options "--trim_poly_g --trim_poly_x -Q -L --correction".
Yes and I believe it should default to skewer without adjusting the pipeline if not other trimmer is set.
Checking the pipeline interface:
{% if sample.trimmer is defined %} --trimmer { sample.trimmer } {% else %} --trimmer "skewer" {% endif %}
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 PEPATAC_log.md
### Adapter trimming: (10-07 11:55:35) elapsed: 0.0 _TIME_
Target to produce: `/home/drc/PEPATAC_OCT_2024/processed/results_pipeline/tutorial1/fastq/tutorial1_R1_trim.fastq`
> `skewer -f sanger -t 4 -m pe -x /home/drc/PEPATAC_OCT_2024//tools/pepatac/tools/NexteraPE-PE.fa --quiet -o /home/drc/PEPATAC_OCT_2024/processed/results_pipeline/tutorial1/fastq/tutorial1 /home/drc/PEPATAC_OCT_2024/processed/results_pipeline/tutorial1/fastq/tutorial1_R1.fastq.gz /home/drc/PEPATAC_OCT_2024/processed/results_pipeline/tutorial1/fastq/tutorial1_R2.fastq.gz` (595646)
Is this helpful?
Isn't skewer the default trimmer?
Isn't skewer the default trimmer?
it is but I prefer trimmomatic!
You can use trimmomatic if you want, but because it's Java, it's not working with Bulker at the moment, so you basically have to put the JAR somewhere and point that ENV var to it, so it will use the local one instead of from within bulker. sorry for the inconvenience, I think I didn't quite finish getting bulker working with java tools, unfortunately.
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