krakenuniq
krakenuniq copied to clipboard
fbreitwieser
Errors running krakenuniq-download - "unexpected end of file" & "dustmasker: command not found"
I ran krakenuniq-download as follows: krakenuniq-download --db krakenU --threads 128 --dust refseq/bacteria $ krakenuniq-download --db krakenU --threads 128 --dust refseq/bacteria Downloading assembly summary file for bacteria genomes, and filtering to assembly level Complete_Genome. WARNING: krakenU/library/bacteria already exists - potentially overwriting files. Downloading bacteria genomes: 362/30955 ... gzip: krakenU/library/bacteria/Complete_Genome/Campylobacter_jejuni_strain_6_1083_19-tax197-GCF_020720295.1_ASM2072029v1_genomic.fna.gz: unexpected end of file 256 at /usr/local/bin/krakenuniq-download line 786. Downloading bacteria genomes: 450/30955 ... gzip: krakenU/library/bacteria/Complete_Genome/Helicobacter_pylori_strain_7_13_D3b-tax210-GCF_002952475.1_ASM295247v1_genomic.fna.gz: unexpected end of file 256 at /usr/local/bin/krakenuniq-download line 786. Downloading bacteria genomes: 452/30955 ... ... gzip: krakenU/library/bacteria/Complete_Genome/Helicobacter_pylori_strain_476_C_EK5-tax210-GCF_006338815.1_ASM633881v1_genomic.fna.gz: unexpected end of file 256 at /usr/local/bin/krakenuniq-download line 786. Downloading bacteria genomes: 17045/30955 ... gzip: krakenU/library/bacteria/Complete_Genome/Cupriavidus_gilardii_strain_nov_21-tax82541-GCF_025643215.1_ASM2564321v1_genomic.fna.gz: not in gzip format 256 at /usr/local/bin/krakenuniq-download line 786. Downloading bacteria genomes: 30955/30955 ... sh: dustmasker: command not found sh: dustmasker: command not found sh: dustmasker: command not found sh: dustmasker: command not found ... sh: dustmasker: command not found Found 30955 files.
