Open dnolin13 opened 1 year ago
AzizHN
commented
1 year ago facing the same problem when I am trying to download all bacteria genomes. Some genomes are downloaded succefully but sometimes it give that error message. I think It's a problem related to the server. Any other opinions please ?
ferreirafm
commented
1 year ago This is worked for me:
wget -t0 https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
lvzenglei
commented
1 year ago That means the network or server is not stable and you can rerun krakenuniq-download and it will skip genomes that exist and download failed genome , when you see 'invalid compressed data--length error' or 'unexpected end of file' in log file ,you can delete the fastq file and rerun krakenuniq-download, This works for me and you can just hava a try~ @dnolin13
Hello! I am getting this issue when installing the databases using this command:
command: /home/delaney/miniconda3/bin/krakenuniq-download --db DBDIR --threads 10 --dust refseq/bacteria refseq/archaea
error:
Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 14240/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 14346/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 14763/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 15612/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 18189/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 18192/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 19248/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 19542/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 19580/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 19604/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Error fetching na/na_genomic.fna.gz. Is curl installed? Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 19921/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 20298/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 20831/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 20860/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 21753/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 22105/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 22777/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 24812/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 25058/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 31020/31487 ... gzip: DBDIR/library/bacteria/Complete_Genome/Endozoicomonas_sp_Mp262-tax2919499-GCF_025643335.1_ASM2564333v1_genomic.fna.gz: not in gzip format Downloading bacteria genomes: 31021/31487 ... 256 at /home/delaney/miniconda3/bin/krakenuniq-download line 773. Downloading bacteria genomes: 31484/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 31486/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Error fetching na/na_genomic.fna.gz. Is curl installed? Error fetching na/na_genomic.fna.gz. Is curl installed? Error fetching na/na_genomic.fna.gz. Is curl installed? Error fetching na/na_genomic.fna.gz. Is curl installed? Error fetching na/na_genomic.fna.gz. Is curl installed? Error fetching na/na_genomic.fna.gz. Is curl installed? Error fetching na/na_genomic.fna.gz. Is curl installed? Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading bacteria genomes: 31487/31487 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Found 31487 files. Skipped download of 31427 files that already existed. Downloading assembly summary file for archaea genomes, and filtering to assembly level Complete_Genome. WARNING: DBDIR/library/archaea already exists - potentially overwriting files. Downloading archaea genomes: 195/497 ... Error fetching na/na_genomic.fna.gz. Is curl installed? Downloading archaea genomes: 497/497 ... Found 497 files. Skipped download of 496 files that already existed.Any help is greatly appreciated!