Comments (8)
Hi Gonçalo,
Hmm, that sounds odd.
Could you try attaching the output from running paleomix?
Also, could you tell me the output from running paleomix --version
?
That should hopefully allow me to narrow down the problem.
Best,
Mikkel
from paleomix.
Hey, sure!
Attached is the output from running paleomix.
When I run paleomix --version
I get paleomix v1.3.6
paleomix output.txt
\1
from paleomix.
That's rather strange:
Java returns the error message Error: Could not find or load main class
, but only when it is run through paleomix.
When you manually tried to run java -server ...
did you also do it in the the paleomix
conda environment?
And if not, could you try activating the paleomix
environment and running the java command again?
Also, could you try to attach your bam_pipeline.ini
file?
Cheers
from paleomix.
Yes, I tried running java -server ...
in the paleomix
conda environment, outside of it java does not run.
My bam_pipeline.ini
is as follows:
[Defaults]
max_threads = 32
log_level = warning
gatk_max_threads = 1
jar_root = /home/gthemudo/miniconda3/envs/paleomix/share/picard-2.27.2-0/
bwa_max_threads = 1
progress_ui = running
temp_root = /tmp/gthemudo/bam_pipeline
jre_options =
bowtie2_max_threads = 1
adapterremoval_max_threads = 1
ui_colors = on
from paleomix.
I noticed that outside the conda environment I seem to still have paleomix v. 1.2.14 installed at ~/install/virtualenvs/paleomix/bin/paleomix although I can't remember how I installed it. Could this be conflicting with the conda instalation?
from paleomix.
I think I found the problem:
Try removing the jre_options =
line from your bam_pipeline.ini
file.
from paleomix.
Yes, that works! Thanks a lot!
from paleomix.
Great!
Empty options in the ini file are supposed to work, but I guess something broke it.
I'll see if I can release a general fix for this.
Thanks for letting me know about this problem, and just open another issue if you run into any other problems!
from paleomix.
Related Issues (20)
- paleomix bam_pipeline: error: unrecognized arguments: --gatk_max_threads=1 --progress_ui=running --jre_options= HOT 5
- ImportError: libhts.so.2: cannot open shared object file: No such file or directory HOT 14
- checkpointing HOT 2
- About the MinQuality setting HOT 6
- BOWTIE2 errors in the pipeline HOT 8
- A problem of PALEOMIX 2.0.0-alpha documentation HOT 2
- Should the .rmdup.collapsed.bam and .rmdup.normal.bam be merged? HOT 1
- biobambam2 instead of picard-tools? HOT 10
- Issue When Employing `RegionsOfInterest`. HOT 6
- similar bams with rescale and non rescale HOT 2
- Phylo pipeline "unknown command" HOT 2
- BWA backtrack additional options added to samse, not aln HOT 3
- conda environment perpetually solving during installation HOT 6
- Errors running node HOT 2
- Error with trimming SE adapters from sample HOT 2
- Receieved a NodeError while running the pipeline HOT 1
- BWA terminated by SIGKILL, PALEOMIX in BAM pipline HOT 2
- Duplicated reads error HOT 3
- Paleomix output reads folder no fastq reads HOT 2
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from paleomix.