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ablab / rnaquast

Quality assessment of de novo transcriptome assemblies from RNA-Seq data
http://cab.spbu.ru/software/rnaquast
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run_busco.py failed for conda busco installation #13

Closed nursyahr closed 1 year ago

nursyahr commented 2 years ago

Dear rnaquast authors,

Thank you for developing this tool.

I am trying to assess quality of my de novo transcriptome with the following command: rnaQUAST.py --transcripts file.cds --busco_lineage busco_downloads/lineages/eudicots_odb10

I have installed and added GeneMark to $PATH. Using the following versions installed via bioconda on ubuntu.

busco                     5.3.2              pyhdfd78af_0    bioconda
rnaquast                  2.0.1                         0    bioconda

I'm unable to run the BUSCO step despite having it installed via conda. Do I need to install the software directly to provide the run_busco.py file? Or can I direct it to the one installed by conda somehow? Here is my log: rnaQUAST.log

Thank you!

andrewprzh commented 2 years ago

Hi

I presume that installation via conda should work just fine. Could you try the latest rnaQUAST version 2.2.2? 2.0.1 is 2 years old and I recall it had some problems with new BUSCO versions.

If the error occurs in the new version, send me also these files: logs can be found in /home/syahirah/plant20/MS_rnaq/logs/MS_trinity.Trinity.okay.Trinity.cds.busco.out.log and /home/syahirah/plant20/MS_rnaq/logs/MS_trinity.Trinity.okay.Trinity.cds.busco.err.log.

All the best Andrey

andrewprzh commented 1 year ago

Please reopen if you still need assistance.

Best Andrey