Downloading plasmid files from FTP...awk: fatal: cannot open file `.listing' for reading
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4 months ago

$ 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 28432 projects (67022 sequences, 118.15 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 11807 projects (14718 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)

Previously i got error with rsync and ftp error which i corrected and used the updated scripts from the kraken2 GitHub directory of script.

But this is a fresh error that i am facing .

Please help me to resolve this issue.

Kraken2 • 309 views
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Please create an issue at kraken2 GitHub site do the developers there can check this error. Perhaps something else has changed at NCBI and they may need to change their rsync script again.

Edit: Looks like you (or someone else) has already created an issue here https://github.com/DerrickWood/kraken2/issues/543

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