Problems with kraken 2 and rsync_from_ncbi.pl

Dear Sir or Madam:

I have got the following error messages:

Encountered problems while solving:
  - nothing provides requested kraken 2.0**

rsync_from_ncbi.pl: unexpected FTP path (new server?) for na

Details are as follows:

https://github.com/bxlab/metaWRAP/blob/master/README.md#installation

Install all metaWRAP dependancies with conda:

(metawrap-env) metaWRAP -h

MetaWRAP v=1.3.2

Firstly, typing the following command

(metawrap-env) mamba install --only-deps -c ursky metawrap-mg

printed the following messages:

Pinned packages:
  - python 2.7.*

Encountered problems while solving:
  - nothing provides cairo 1.14.8.* needed by metawrap-mg-1.0-0

Secondly, typing the following command

# OR
mamba install biopython blas=2.5 blast=2.6.0 bmtagger bowtie2 bwa checkm-genome fastqc kraken=1.1 kraken=2.0 krona=2.7 matplotlib maxbin2 megahit metabat2 pandas prokka quast r-ggplot2 r-recommended salmon samtools=1.9 seaborn spades trim-galore

printed the following messages:

Pinned packages:
  - python 2.7.*

Encountered problems while solving:
  - nothing provides requested kraken 2.0**

Thirdly, I typed the following command (omitting kraken=2.0).

# OR
mamba install biopython blas=2.5 blast=2.6.0 bmtagger bowtie2 bwa checkm-genome fastqc kraken=1.1 krona=2.7 matplotlib maxbin2 megahit metabat2 pandas prokka quast r-ggplot2 r-recommended salmon samtools=1.9 seaborn spades trim-galore

https://github.com/bxlab/metaWRAP/blob/master/installation/database_installation.md#downloading-the-kraken1-standard-database Downloading the KRAKEN1 standard database:

Running the command on this page printed the following messages: standard output

Found jellyfish v1.1.12
Downloaded accession to taxon map(s)
Downloaded taxonomy tree data
Uncompressing taxonomy data... done.
Untarring taxonomy tree data... done.

standard error

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

https://github.com/bxlab/metaWRAP/issues/449

Following the comments on this github page, I changed the files as follows:

${HOME}/miniconda3/envs/mambaEnv/envs/metawrap-env/libexec/download_genomic_library.sh

33c33
< FTP_SERVER="ftp://$NCBI_SERVER"
---
> FTP_SERVER="https://$NCBI_SERVER"

${HOME}/miniconda3/envs/mambaEnv/envs/metawrap-env/libexec/rsync_from_ncbi.pl

37c37
<   if (! ($full_path =~ s#^ftp://ftp\.ncbi\.nlm\.nih\.gov/genomes/##)) {
---
>   if (! ($full_path =~ s#^https://ftp\.ncbi\.nlm\.nih\.gov/genomes/##)) {
55c55
<         s/^/ftp:\/\/ftp.ncbi.nlm.nih.gov\/genomes\//;
---
>         s/^/https:\/\/ftp.ncbi.nlm.nih.gov\/genomes\//;

Then, running the command

kraken-build --standard --threads 24 --db MY_KRAKEN_DATABASE

printed the following messages: standard output

Found jellyfish v1.1.12

standard error

Step 1/3: performing rsync dry run...
Rsync dry run complete, removing any non-existent files from manifest.
Step 2/3: Performing rsync file transfer of requested files
Rsync file transfer complete.
Step 3/3: Assigning taxonomic IDs to sequences
Processed 506 projects (910 sequences, 1.43 Gbp)... done.
All files processed, cleaning up extra sequence files... done, library complete.
rsync_from_ncbi.pl: unexpected FTP path (new server?) for na

I found the following two pages but could not find how to solve this problem.

Any comments will be gratefully appreciated.

bxlab / metaWRAP

Problems with kraken 2 and rsync_from_ncbi.pl #479