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marbl / Mash

Fast genome and metagenome distance estimation using MinHash
mash.readthedocs.org
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mash dist #151

Open yirui0214 opened 4 years ago

yirui0214 commented 4 years ago

I am new to linux. When I run mash dist, I meet a trouble as the follow

mash dist refseq.genomes.k21.s1000.msh 19-40.random.fq.gz.msh > 19-40.distances.tab ERROR: could not open "refseq.genomes.k21.s1000.msh" for reading.

Can you give me some suggestions?

yirui0214 commented 4 years ago

The database has been successfully saved.

wget https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh --2020-11-21 18:00:35-- https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh Connecting to 10.53.6.245:3128... connected. Proxy request sent, awaiting response... 301 Moved Permanently Location: https://obj.umiacs.umd.edu/marbl_publications/mash/refseq.genomes.k21s1000.msh [following] --2020-11-21 18:00:37-- https://obj.umiacs.umd.edu/marbl_publications/mash/refseq.genomes.k21s1000.msh Connecting to 10.53.6.245:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 754115096 (719M) [model/mesh] Saving to: ‘refseq.genomes.k21s1000.msh’

refseq.genomes.k21s1000.msh 100%[=====================================================>] 719.18M 6.84MB/s in 10m 1s

2020-11-21 18:10:40 (1.20 MB/s) - ‘refseq.genomes.k21.s1000.msh’ saved [754115096/754115096]

nsarode-joyn commented 3 years ago

the only time I have faced this issue is when I didn't give the right path to the sketch database. You could give complete path to the location where the sketch is downloaded (use pwd to get the path)