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sanger-pathogens / seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads
https://sanger-pathogens.github.io/seroba/
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Can't build DB? False | ariba prepare_ref | no such file #37

Open tseemann opened 5 years ago

tseemann commented 5 years ago 
False
no such file
ariba prepareref -f /home/linuxbrew/db/temp_aribaX5nkguz0r/temp_fasta_ref.fasta -m /home/linuxbrew/db/temp_aribaX5nkguz0r/temp_meta_ref.tsv --cdhit_clusters /home/linuxbrew/db/temp_aribaX5nkguz0r/cdhit_cluster_ref seroba/ariba_db/01/ref
False
no such file
ariba prepareref -f /home/linuxbrew/db/temp_aribaXxkf8ld23/temp_fasta_ref.fasta -m /home/linuxbrew/db/temp_aribaXxkf8ld23/temp_meta_ref.tsv --cdhit_clusters /home/linuxbrew/db/temp_aribaXxkf8ld23/cdhit_cluster_ref seroba/ariba_db/02/ref
False
no such file
ariba prepareref -f /home/linuxbrew/db/temp_aribaXhf22fy64/temp_fasta_ref.fasta -m /home/linuxbrew/db/temp_aribaXhf22fy64/temp_meta_ref.tsv --cdhit_clusters /home/linuxbrew/db/temp_aribaXhf22fy64/cdhit_cluster_ref seroba/ariba_db/03/ref
False
no such file
ariba prepareref -f /home/linuxbrew/db/temp_aribaXkkhn_2b7/temp_fasta_ref.fasta -m /home/linuxbrew/db/temp_aribaXkkhn_2b7/temp_meta_ref.tsv --cdhit_clusters /home/linuxbrew/db/temp_aribaXkkhn_2b7/cdhit_cluster_ref seroba/ariba_db/04/ref
False
antunderwood commented 5 years ago

+1 I get the same thing after installation via conda

antunderwood commented 5 years ago

It works if you include a trailing slash!!

seroba createDBs DB/ 71

This can be solved by replacing all instances of os.path.dirname(self.out_dir) with self.out_dir in the file ref_db_creator.py.

See this PR https://github.com/sanger-pathogens/seroba/pull/38

tseemann commented 5 years ago

Thanks Ant! @aunderwo

VoronDM commented 4 years ago

Hi! seroba createDBs database/ 71 many ignored sequences in ariba output and "no such file" warnings.

total.log

For example ariba_db folder contain such files:

DB_part.zip