ablab
License issue
Hello, I am trying to run metaquast through my university's HPC system. The system has both quast v 5.2.0 and genemark_s v 2012.04 available. However, when running this command with both modules loaded I receive the following warning:
metaquast.py
--threads 14
--gene-finding
-o $ANALYSIS_FOLDER/assembly/assembly_stats/$(basename ${i%.1*})
-l megahit,SPAdes
$ANALYSIS_FOLDER/assembly/megahit/$(basename ${i%.1*})/megahit_final.contigs.fa
$ANALYSIS_FOLDER/assembly/spades/$(basename ${i%.1*})/contigs.fasta \
2024-06-21 14:05:22 WARNING: GeneMark tool can't be started because of license limitations!
NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
The rest of the command works as expected with the exception of Drawing interactive Krona plots which I know is a known bug. Unfortunately the --no-krona option isn't supported on my system but that is a separate problem. My HPC is again hosted by an American university and thus shouldn't have this license restriction. Please let me know what solutions or work arounds are available.
I know this is was posted a whole term pregnancy ago but I have been trying to fix this for several hours tonight, as I have just installed GeneMark (including the license). I found this explanation for the bioconda installation of quast, which I am using.
There is a solution in that post, but I didn't do it right. I hacked around and got it to run GeneMark and find the license but it is passing incorrect arguments to one of the tools inside it.
Your error is coming from this line in the code, which will always quit if the variable is set to True, as in the bioconda distribution.
