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AstrobioMike / GToTree

A user-friendly workflow for phylogenomics
GNU General Public License v3.0
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Error:Is the internet connection weak? #32

Closed agavriilidou closed 3 years ago

agavriilidou commented 3 years ago

Hi!

I have installed GToTree v1.5.47 with miniconda3 and I am trying to run it with some test data but I get this error.

 GToTree v1.5.47 (github.com/AstrobioMike/GToTree)

 ---------------------------------  RUN INFO  --------------------------------- 

    Command entered:
    /tools/software/bioinfo-tools/miniconda/miniconda3/envs/gtotree/bin/GToTree -A fasta_files.txt -a GTDB-Desulfobacterota_D-phylum-GTDB-rep-accs.txt -H Bacteria -o gtotree_output -D

    Input genome sources include:
      - NCBI accessions listed in GTDB-Desulfobacterota_D-phylum-GTDB-rep-accs.txt (17 genomes)
      - Amino acid files listed in fasta_files.txt (4 genomes)

                             Total input genomes: 21

    HMM source to be used:
      - Bacteria (74 targets)

    Options set:
      - The output directory has been set to "gtotree_output/".
      - GTDB taxonomic info will be added to labels where possible.

 ############################################################################## 
 ####          Working on the genomes provided as NCBI accessions          ####
 ############################################################################## 

          Downloading GenBank assembly summaries...

  Download of NCBI assembly summaries failed :(
  Is the internet connection weak?

Exiting for now.

Any ideas?

Thanks in advance.

AstrobioMike commented 3 years ago

Hey there :)

Thanks for trying GToTree. Sorry for the snag :/

That should only pop up if it's not able to download the NCBI assembly info. Can you try running just this command in the same environment and let me know if that works? 

curl --connect-timeout 30 --retry 10 ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt -o ncbi_assembly_info.tmp

And if not, then trying this one:

curl --connect-timeout 30 --retry 10 https://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt -o ncbi_assembly_info.tmp

It's possible ftp isn't available in the environment, and if so, adding the -P flag to the GToTree command will try to do things through http like the second command here does.