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davidebolo1993 / VISOR

VarIant SimulatOR for short, long and linked reads
GNU Lesser General Public License v3.0
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"[Error] minimap2 must be in PATH", but it is #21

Closed ngaitan55 closed 2 years ago

ngaitan55 commented 2 years ago

Hi, I´m having issues when running VISOR Laser with the following command:

VISOR LASeR -g Athaliana_ref.fa -s hack.out -b shorts.laser.simple.bed -o 60xONT_100.out --threads 8 --coverage 60 --tag --read_type nanopore --error_model nanopore2020 --qscore_model nanopore2020

I don´t understand why this happens because doing a simple:

echo $PATH

yields:

/home/nicolasggg/meme/bin:/home/nicolasggg/meme/libexec/meme-5.4.1:/home/nicolasggg/bioinformatic_software/minimap2/minimap2:/home/nicolasggg/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/bin:/usr/lib/jvm/default/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl:/var/lib/snapd/snap/bin

where you can see that the minimap2 binary executable is effectively on the PATH variable. I can also run minimap2 separately so this error does not make sense. I would much appreciate it if you could help me. Thanks!

ngaitan55 commented 2 years ago

It was an issue with the minimap2 installation. Ill close this thread