Kraken2

Question

[Ap1438]

I wanted to make a kraken database but i got this error while running the command.
I am using Kraken2

$ kraken2-build --standard --threads 24 --db kraken2database/
Downloading nucleotide gb accession to taxon map... done.   
Downloading nucleotide wgs accession to taxon map... done.   
Downloaded accession to taxon map(s)   
Downloading taxonomy tree data... done.   
Uncompressing taxonomy data... done.   
Untarring taxonomy tree data... done.   
rsync_from_ncbi.pl: unexpected FTP path (new server?) for https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/762/265/GCF_000762265.1_ASM76226v1

.
Can anyone help me to resolve this issue.

[GenoMax]

Are you using the latest version of kraken2? If not it would help to upgrade.

rsync_from_ncbi.pl was updated yesterday so you may want to try using that version.

[Ap1438]

Downloading nucleotide gb accession to taxon map...Downloading nucleotide gb accession to taxon map... done.
Downloading nucleotide wgs accession to taxon map... done.
Downloaded accession to taxon map(s)
Downloading taxonomy tree data... done.
Uncompressing taxonomy data... done.
Untarring taxonomy tree data... done.
Step 1/2: Performing rsync file transfer of requested files
Rsync file transfer complete.
Step 2/2: Assigning taxonomic IDs to sequences
All files processed, cleaning up extra sequence files... done, library complete.
Masking low-complexity regions of downloaded library... done.
Step 1/2: Performing rsync file transfer of requested files
Rsync file transfer complete.
Step 2/2: Assigning taxonomic IDs to sequences
All files processed, cleaning up extra sequence files... done, library complete.
Masking low-complexity regions of downloaded library... done.
Step 1/2: Performing rsync file transfer of requested files
Rsync file transfer complete.
Step 2/2: Assigning taxonomic IDs to sequences
All files processed, cleaning up extra sequence files... done, library complete.
Masking low-complexity regions of downloaded library... done.
Downloading plasmid files from FTP...

Due to some network issue it got canceled here.But i reran the command as its mentioned in the manual that it will resume from the last checkpoint.

But this time i got this error

Step 1/2: Performing rsync file transfer of requested files
Rsync file transfer complete.
Step 2/2: Assigning taxonomic IDs to sequences
All files processed, cleaning up extra sequence files... done, library complete.
Masking low-complexity regions of downloaded library... done.
rsync: change_dir "/refseq/bacteria" (in genomes) failed: No such file or directory (2)
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1816) [Receiver=3.2.3]
Error downloading assembly summary file for bacteria, exiting.

[GenoMax]

Did you download a new version of the perl script and replaced it in your install of Kraken?

[Ap1438]

yes i have replaced it

[GenoMax]

Are you still getting the error? If so you may want to open an issue at kraken2 github site.

[Ap1438]

$ kraken2-build --standard --threads 12 --db kraken2db/
Downloading nucleotide gb accession to taxon map... done.
Downloading nucleotide wgs accession to taxon map... done.
Downloaded accession to taxon map(s)
Downloading taxonomy tree data... done.
Uncompressing taxonomy data... done.
Untarring taxonomy tree data... done.
Step 1/2: Performing rsync file transfer of requested files
Rsync file transfer complete.
Step 2/2: Assigning taxonomic IDs to sequences
Processed 425 projects (720 sequences, 1.15 Gbp)... done.
All files processed, cleaning up extra sequence files... done, library complete.
Masking low-complexity regions of downloaded library... done.
Step 1/2: Performing rsync file transfer of requested files
Rsync file transfer complete.
Step 2/2: Assigning taxonomic IDs to sequences
Processed 28374 projects (66863 sequences, 117.87 Gbp)... done.
All files processed, cleaning up extra sequence files... done, library complete.
Masking low-complexity regions of downloaded library... done.
Step 1/2: Performing rsync file transfer of requested files
Rsync file transfer complete.
Step 2/2: Assigning taxonomic IDs to sequences
Processed 11808 projects (14719 sequences, 463.50 Mbp)... done.
All files processed, cleaning up extra sequence files... done, library complete.
Masking low-complexity regions of downloaded library... done.
Downloading plasmid files from FTP...awk: fatal: cannot open file `.listing' for reading (No such file or directory).

I made some changes in the script and the previous error was rectified but this time i got new error related to plasmid.

Answer 1

[Mehmet]

Maybe the path to the data in the script rsync_from_ncbi.pl has changed? Can you check the path on the script whether it is still valid? If not , you need to find the correct path (where the data is deposited) and replace it the current one in the script.

[Ap1438]

path is still valid