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zy-optimistic / GAEP

A genome assembly assessment pipeline.
GNU General Public License v3.0
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Error Message when running Merqury #13

Open lingvv opened 9 months ago

lingvv commented 9 months ago

Greetings! I kindly request your guidance in addressing this error. Your assistance is greatly appreciated.

Additionally, I believe it would be highly beneficial if your team could enhance the documentation related to tool usage. As a user with limited prior experience in Busco and Merqury, I encounter challenges in formulating the correct commands for tool execution. A more comprehensive documentation would greatly assist users like myself.

(base) rndvivien@SG-LP-7469:~/GAEP$ ./gaep kacc run_merqury -r <assembled_genome.fasta> -i <forward_illumina.fq.gz> -i
<reverse_illumina.fq.gz> -g <genome_size> -d <output_directory>
readline() on unopened filehandle at /home/rndvivien/GAEP/scripts/run_merqury.pl line 51.

[run_merqury] Output directory is gaep_merqury_pm1_.
[run_merqury] Error! Meryl is not found.
[run_merqury] Check your config file or set it in your environment.
zy-optimistic commented 8 months ago

Merqury relies on Meryl for k-mer counting, so please install Meryl and ensure that its path is added to the cconfig file or your environment.