Viral neighbors download (Died)

[jalalsiddiqui]

I tried to create the viral neighbors database by this line

krakenuniq-download --db DB 'viral-neighbors' --rettype fasta -R --rsync

I get the following output.

Downloading viral neighbors. Downloading DB/taxonomy/nucl_gb.accession2taxid.gz [curl -g 'https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz' -o 'DB/taxonomy/nucl_gb.accession2taxid.gz'] ... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 2283M 100 2283M 0 0 46.5M 0 0:00:49 0:00:49 --:--:-- 63.6M done (49s) DB/taxonomy/nucl_gb.accession2taxid.gz check [2.23 GB] SUCCESS Sorting maping file (will take some time) [gunzip -c DB/taxonomy/nucl_gb.accession2taxid.gz | cut -f 1,3 > DB/taxonomy/nucl_gb.accession2taxid.sorted.tmp && sort --parallel 5 -T DB/taxonomy DB/taxonomy/nucl_gb.accession2taxid.sorted.tmp > DB/taxonomy/nucl_gb.accession2taxid.sorted && rm DB/taxonomy/nucl_gb.accession2taxid.sorted.tmp] ... done (4m21s) DB/taxonomy/nucl_gb.accession2taxid.sorted check [4.77 GB] Reading names file ... DB/library/viral/Neighbors/esearch_res.jsonDownloading 188678 sequences into DB/library/viral/Neighbors. query_key=1&webenv=MCID_65fc9daa6ac4157b854fce08 Downloading sequences 1 to 10000 of 188678 ... done Downloading sequences 10001 to 20000 of 188678 ...https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=taxonomy&id=MT254063 MT254063: 239365 [*]

No mapping for sequence MT254063 - not writing it to it's own file! https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=taxonomy&id=MT254062 MT254062: 239365 [*]

No mapping for sequence MT254062 - not writing it to it's own file! https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=taxonomy&id=MT254061 MT254061: 239365 [*]

No mapping for sequence MT254061 - not writing it to it's own file! done Downloading sequences 20001 to 30000 of 188678 ...https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=taxonomy&id=MT598195 MT598195: 239365 [*]

No mapping for sequence MT598195 - not writing it to it's own file! https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=taxonomy&id=AC_000192 AC_000192: 11144 [] done Downloading sequences 30001 to 40000 of 188678 ... done Downloading sequences 40001 to 50000 of 188678 ...https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=taxonomy&id=MK559457 MK559457: 239365 []

No mapping for sequence MK559457 - not writing it to it's own file! done Downloading sequences 50001 to 60000 of 188678 ...https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=taxonomy&id=MK210250 MK210250: 239365 [*]

No mapping for sequence MK210250 - not writing it to it's own file! https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=taxonomy&id=MK164400 MK164400: 239365 [*]

No mapping for sequence MK164400 - not writing it to it's own file! done Downloading sequences 60001 to 70000 of 188678 ... done Downloading sequences 70001 to 80000 of 188678 ... done Downloading sequences 80001 to 90000 of 188678 ...https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=taxonomy&id=KU980912 KU980912: 239365 [*]

No mapping for sequence KU980912 - not writing it to it's own file! https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=taxonomy&id=KU980911 KU980911: 239365 [*]

No mapping for sequence KU980911 - not writing it to it's own file! https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=taxonomy&id=KU980910 KU980910: 239365 [*]

No mapping for sequence KU980910 - not writing it to it's own file! done Downloading sequences 90001 to 100000 of 188678 ...https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=taxonomy&id=HM104174 Use of uninitialized value $taxid in concatenation (.) or string at /path/to/miniconda3/envs/krakenuniq/bin/krakenuniq-download line 443. HM104174: [*]

No taxid mapping for sequence HM104174! Died at /path/to/miniconda3/envs/krakenuniq/bin/krakenuniq-download line 517.