Downloading plasmid files from FTP...awk: fatal: cannot open file `.listing' for reading (No such file or directory)

[ap1438]

Kraken.zip
$ 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 have attached all the files present in the script directory as ZIP file.Please check if needed.

I got this error while creating the database. Can anyone help me with this.

[lconteville]

I've got the same error

[SergeyBaikal]

Were you able to solve the problem?

[stephenqub]

I have the same error. Has anyone been able to solve this?

[SergeyBaikal]

stephenqub,
Have you tried changing the script? #529 (comment)
I tried it. Plasmid and virus databases are downloaded, but the error is the same.
Downloading plasmid file manifest from FTP...awk: cannot open .listing (No such file or directory)

[tseemann]

Possible solution here: #532

[TDDB-limagrain]

Possible solution as well here: #412 (comment)
It worked for me.

[ashdederich]

I'm trying to use kraken2-build to download the databases. My download stops at the same plasmid error.

@tseemann I've made the changes suggested in #532

I've changed line 47 of the download_genomic_library.sh according to #532 (comment)

I've changed ftp to https in line 46 in the file rsync_from_ncbi.pl according to #532 (comment)

And I've tried your solution for the rsync_from_ncbi.pl #532 (comment)

I'm still getting the same error, running the command:

kraken2-build --db kraken-db/ --download-library plasmid --use-ftp

And get the error:

Downloading plasmid files from FTP...awk: fatal: cannot open file `.listing' for reading: No such file or directory

What's going on? Any suggestions?

[TDDB-limagrain]

Hi @ashdederich ,
modify the download_genomic_library.sh script according to #412 (comment).
Comment the wget -q --no-remove-listing --spider $FTP_SERVER/genomes/refseq/plasmid/ line and add just after that:

   curl -s $FTP_SERVER/genomes/refseq/plasmid/ \
        | perl -nle 'print  "$1"  while (/<a\s+href\s*=\s*"([^"]+.gz)"/g)' \
        | sort -u \
        > .listing

[SergeyBaikal]

Why all these manipulations? Everything is ready, you just need to download the database to your taste.

https://benlangmead.github.io/aws-indexes/k2

[ashdederich]

@TDDB-limagrain Thank you! That fixed it.

@SergeyBaikal Well, I had an error pop up when running kraken2-build, I googled the error, and it brought me here where possible solutions were linked. Thank you for linking the indexes page - I was unaware that it existed.