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marbl / merqury

k-mer based assembly evaluation
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Issue with link... #35

Closed francoissabot closed 3 years ago

francoissabot commented 3 years ago

Hi all

I have containerized my merqury to be able to test it from anywhere, but I am facing issues with link when launching mercury.sh:

""" Singularity> echo $MERCURY /opt/tools/merqury-1.1 Singularity> $MERCURY/merqury.sh tog7291FlyeRacon3Medaka.meryl tog7291FlyeRacon3Medaka.fasta MerquryOutput /opt/tools/merqury-1.1/merqury.sh: line 16: /merqury-1.1//util/util.sh: No such file or directory link: missing operand after 'tog7291FlyeRacon3Medaka.meryl' Try 'link --help' for more information. read:

No haplotype dbs provided. Running Merqury in non-trio mode...

link: missing operand after 'tog7291FlyeRacon3Medaka.fasta' Try 'link --help' for more information. asm1: out : MerquryOutput

mkdir: cannot create directory 'logs': Read-only file system

Get spectra-cn plots and QV stats /opt/tools/merqury-1.1/merqury.sh: line 71: logs/MerquryOutput.spectra-cn.log: No such file or directory Singularity> """

Does anyone have an idea ? I am in a writable folder, and the link command ask for two parameters, the source and the target

The container is based on ubuntu 20.04

arangrhie commented 3 years ago

Export the merqury env var to $MERQURY, not $MERCURY.

francoissabot commented 3 years ago

ok my fault RTFM ^^

Thanks