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DRL / blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
GNU General Public License v3.0
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error in uniprot parallel download #87

Closed raw937 closed 4 years ago

raw937 commented 5 years ago

Download database

wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Reference_Proteomes_2019_02.tar.gz

Unpack protein FASTAs for each kingdom

parallel -j4 'gunzip {}' ::: `ls | grep "fasta.gz" | grep -v 'DNA' | grep -v 'additional'

The unpacking of fasta's isn't working. /var/spool/slurmd/job8046023/slurm_script: line 18: unexpected EOF while looking for matching ``' /var/spool/slurmd/job8046023/slurm_script: line 33: syntax error: unexpected end of file

Any thoughts?

DRL commented 4 years ago

Could be that you did not download the complete file...

I would look at what is happening in line 18 and 33 of your slurm script...

cheers,

dom