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hildebra / lotus2

Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
http://lotus2.earlham.ac.uk/
GNU General Public License v3.0
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Can't open myTestRun/tmpFiles//RDPotus.tax : #72

Closed Natalie-koks closed 2 weeks ago

Natalie-koks commented 2 weeks ago

I am trying to run the example command : lotus2 -i ~/miniconda3/pkgs/lotus2-2.32-hdfd78af_1/share/lotus2-2.32-1/Example/ -m ~/miniconda3/pkgs/lotus2-2.32-hdfd78af_1/share/lotus2-2.32-1/Example/miSeqMap.sm.txt -o myTestRun It starts running smoothly, creates the myTestRun folder but breaks after this point,

"00:00:14 Assigning taxonomy with RDP"

This is the error I get. It is unable to create the RDPotus file. Can't open myTestRun/tmpFiles//RDPotus.tax : No such file or directory at /home/Users/nk62/miniconda3/envs/analysis/bin/lotus2 line 4502. Wondering if there is something I am particularly doing wrong. Any help?

hildebra commented 2 weeks ago

Hey Natalie, this is probably related to java JRE not being installed on the system. can you check in the LotuSLogs/LotuS_progout.log file for the error that the program was producing? if it is related to java, you need to install jre in your conda environment, e.g. this might be a good start: https://anaconda.org/bioconda/java-jdk hth, Falk

Natalie-koks commented 2 weeks ago

Thank you very much