No preliminary seqid/taxid mapping files found, aborting.

[fjptwenger]

when I build nr database ，the error：

$ kraken2-build --build  --db ~/software/metadb 
Creating sequence ID to taxonomy ID map (step 1)...
No preliminary seqid/taxid mapping files found, aborting.

I don't know how to solve this problem。

[jenniferlu717]

How did you download/build the database?

[fjptwenger]

that command： kraken2-build --download-taxonomy --threads 8 --protein --db ~/software/metadb/ --use-ftp

[fjptwenger]

I deleted the original directory and re-downloaded and now encountered this error:

Untarring taxonomy tree data...
gzip: stdin: invalid compressed data--format violated
tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now

and I download taxdump.tar.gz from NCBI instead of the kraken2 download taxdump.tar.gz file，and run**kraken2-build --download-taxonomy --threads 8 --protein --db ~/software/metadb/ --use-ftp ** again .it show below：

Untarring taxonomy tree data... done.

then the nr database download before and move in library/nr,now the Directory Structure：

├── library
│   └── nr
│       └── nr.gz
└── taxonomy
    ├── accmap.dlflag
    ├── citations.dmp
    ├── delnodes.dmp
    ├── division.dmp
    ├── gc.prt
    ├── gencode.dmp
    ├── merged.dmp
    ├── names.dmp
    ├── nodes.dmp
    ├── prelim_map.txt
    ├── prot.accession2taxid
    ├── readme.txt
    ├── taxdump.dlflag
    ├── taxdump.tar.gz
    ├── taxdump.untarflag

but error still exist:

$ kraken2-build --build  --db ~/software/metadb 
Creating sequence ID to taxonomy ID map (step 1)...
No preliminary seqid/taxid mapping files found, aborting.

[jenniferlu717]

How did you download the nr.gz library file?

[freixas84]

Hi, I am stuck in the same error, but with the nt database. Both the nt and taxonomy files were downloaded as per below:

kraken2-build --use-ftp --download-taxonomy --db nt
kraken2-build --use-ftp --download-library nt --db nt --threads 12

The error I get after attempting to build the libraries is as follows:
Creating sequence ID to taxonomy ID map (step 1)...
No preliminary seqid/taxid mapping files found, aborting.

Any help will be very appreciated!

[Sevgi-k]

Hi, I am stuck in the same error as well... Did anybody find a solution?

[Solenyalyl]

I'm stucked too. anyone can help?

[LiZhihua1982]

@fjptwenger Hi would you solve this problem?

[dannyionescu]

Same problem today with the nt DB.
I downloaded the files manually again and they look the same.

accession accession.version taxid gi
A00001 A00001.1 10641 58418
A00002 A00002.1 9913 2
A00003 A00003.1 9913 3
A00004 A00004.1 32630 57971
A00005 A00005.1 32630 57972
A00006 A00006.1 32630 57973
A00008 A00008.1 32630 57974
A00009 A00009.1 32630 57975
A00010 A00010.1 32630 57976
A00011 A00011.1 32630 57977
A00012 A00012.1 32630 57978
A00013 A00013.1 32630 57979
A00014 A00014.1 32630 57980
A00015 A00015.1 32630 57981
A00016 A00016.1 32630 57982

If there is a solution, please let me know.
Thanks

[tpellegrinetti]

Any solution? I need to solve this problem

[dannyionescu]

Not from my side, I am still waiting for answers.
I tried to treat the nt fasta file as new data and add it to the db but it complained about something else.

[sapuizait]

same here when trying to build the NT - it has downloaded the nt.gz and the taxonomy in a separate folder and gives the same error!

• is there no solution?

[jsalas0798]

Hi is there any solution to this problem, when i run this command line kraken2-build --build --db database it prompts:

Creating sequence ID to taxonomy ID map (step 1)...
No preliminary seqid/taxid mapping files found, aborting.

For the download of taxonomy i used: kraken2-build --download-taxonomy --db database
and for the download of the library: kraken2-build --download-library bacteria --db database

[tpellegrinetti]

I solved this problem using kaiju instead kraken2

[rturba]

Damn, just encountered the same issue. I guess this is a dead end :/

[diogopaes1]

I also stopped at this problem. It seems that you need to convert the assembly_summary.txt files to the .fna format within the db/library folder. Or download manually.