Paleomix can not find picard even though it is there

[themudo]

Hi, I am having some problems with paleomix. I recently uninstalled paleomix and reinstalled (with conda) the latest version, created the symlink to picard at ~/install/jar_root/picard.jar and even changed the ~/.paleomix/bam_pipeline.ini option to direct paleomix directly to my picard.jar file. If I run "java -server -Djava.io.tmpdir=/tmp/gthemudo/bam_pipeline -Djava.awt.headless=true -XX:+UseSerialGC -Xmx4g -jar /home/gthemudo/install/jar_root/picard.jar MarkDuplicates --version" on the command line I get "Version:2.27.2" as response. Any idea what is causing this? Cheers, Gonçalo

[MikkelSchubert]

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

[themudo]

Hey, sure! Attached is the output from running paleomix. When I run paleomix --version I get paleomix v1.3.6 paleomix output.txt \1

[MikkelSchubert]

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

[themudo]

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

[themudo]

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?

[MikkelSchubert]

I think I found the problem:

Try removing the jre_options = line from your bam_pipeline.ini file.

[themudo]

Yes, that works! Thanks a lot!

[MikkelSchubert]

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!