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.

[jalalsiddiqui]

Of note, I just want to download the viral neighbors fasta files and I can make the mapping files on my own.

[xapple]

I just got the same problem, and hence can't get the refseq/viral/Any viral-neighbors database for my analysis.

Downloading sequences 110001 to 120000 of 188670 ... done
Downloading sequences 120001 to 130000 of 188670 ... done
Downloading sequences 130001 to 140000 of 188670 ... done
Downloading sequences 140001 to 150000 of 188670 ... done
Downloading sequences 150001 to 160000 of 188670 ... done
Downloading sequences 160001 to 170000 of 188670 ...https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=taxonomy&id=AF026278
AF026278: 196400 [/tmp/I9cCOqUDe_]
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=taxonomy&id=AF035006
Use of uninitialized value $taxid in concatenation (.) or string at /home/abf24779/.conda/envs/tools/bin/krakenuniq-download line 443.
AF035006: [/tmp/hwfmJBWRQ]
No taxid mapping for sequence AF035006!
Died at /home/abf24779/.conda/envs/tools/bin/krakenuniq-download line 517.

I see that the last message from this thread was from months ago. Is krakenuniq not being maintained anymore? Should it be considered obsolete?