amrfinder_update cannot connect to FTP and thus download #bug #help #120

geboro · 2023-05-04T16:16:22Z

Hello,

I'm struggling installing AMRFinder in my institution. It keeps failing because it cannot find the ftp site:

amrfinder_update  --database /home/bioinf/bioinf_archive/98_mökiDatabases/bakta/db/amrfinderplus-db
Running: amrfinder_update --database /home/bioinf/bioinf_archive/98_mökiDatabases/bakta/db/amrfinderplus-db
Looking up the published databases at https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/

*** ERROR ***
CURL: Cannot read from https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/

HOSTNAME: ?
SHELL: /bin/bash
PWD: /home/bioinf
PATH: /home/bioinf/mambaforge/envs/bakta/bin:/home/bioinf/mambaforge/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
Progam name:  amrfinder_update
Command line: amrfinder_update --database /home/bioinf/bioinf_archive/98_mökiDatabases/bakta/db/amrfinderplus-db

but curl is working fine:

curl https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
<html>
 <head>
  <title>Index of /pathogen/Antimicrobial_resistance/AMRFinderPlus/database</title>
 </head>
 <body>
<h1>Index of /pathogen/Antimicrobial_resistance/AMRFinderPlus/database</h1>
<pre>Name                                              Last modified      Size  <hr><a href="/pathogen/Antimicrobial_resistance/AMRFinderPlus/">Parent Directory</a>                                                       -   
<a href="3.10/">3.10/</a>                                             2021-12-22 13:07    -   
<a href="3.2/">3.2/</a>                                              2019-10-31 11:24    -   
<a href="3.6/">3.6/</a>                                              2020-03-25 08:36    -   
<a href="3.8/">3.8/</a>                                              2020-10-02 15:43    -   
<a href="3.9/">3.9/</a>                                              2020-12-21 10:09    -   
<a href="3.10/">3.10/</a>                                              2022-10-12 10:00    -
<a href="3.11/">3.11/</a>                                              2022-10-12 10:00    -
<a href="latest/">latest/</a>                                             2021-12-22 13:19    -   
<hr></pre>

So two questions:

Is there any way to separate database installation from download?
I downloaded and indexed the databases manually, but when I run 'amrfinder' it cannot find the path of the databases by default. Since I am working with a wrapper that I cannot edit, and the binaries in AMRFinder are uneditable, is there any way to change the default path where amrfinder looks for the database?

Thanks.

The text was updated successfully, but these errors were encountered:

vbrover · 2023-05-04T16:18:41Z

Can you run this command?

amrfinder -u

vbrover · 2023-05-04T16:38:24Z

This URL is accessible: https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/

vbrover · 2023-05-04T16:44:25Z

Is there any way to separate database installation from download?

There is no separate step "installation".
There are 2 steps:

download the files from FTP;
index them.

I downloaded and indexed the databases manually,

If the files are downloaded manually then they can be indexed by amrfinder_index.

https://github.com/ncbi/amr/wiki/Upgrading#database-updates

is there any way to change the default path where amrfinder looks for the database?

amrfinder -d DATABASE_DIR

evolarjun · 2023-05-04T17:31:06Z

I think Slava covered it above, but just wanted to add pointers to the documentation for amrfinder_index and amrfinder_update:

Please let us know if you are still having trouble or if you managed to get it working in case others are having this issue.

geboro · 2023-05-05T09:55:06Z

Can you run this command?
amrfinder -u

No. This gives the following error:

Running: amrfinder -u
Software directory: '/home/bioinf/mambaforge/envs/bakta/bin/'
Software version: 3.11.11
Running: /home/bioinf/mambaforge/envs/bakta/bin/amrfinder_update -d /home/bioinf/mambaforge/envs/bakta/share/amrfinderplus/data
Looking up the published databases at https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/

*** ERROR ***
CURL: Cannot read from https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/

HOSTNAME: ?
SHELL: /bin/bash
PWD: /home/bioinf/bioinf_data/57_boge/Erwinia_tasmaniensis/Genomes/seti_Erwinia_tasmaniensis_54G
PATH: /home/bioinf/mambaforge/envs/bakta/bin:/home/bioinf/mambaforge/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
Progam name:  amrfinder_update
Command line: /home/bioinf/mambaforge/envs/bakta/bin/amrfinder_update -d /home/bioinf/mambaforge/envs/bakta/share/amrfinderplus/data

*** ERROR ***
'/home/bioinf/mambaforge/envs/bakta/bin/amrfinder_update'  -d '/home/bioinf/mambaforge/envs/bakta/share/amrfinderplus/data' > /tmp/amrfinder.8rWEYL/log
status = 256


HOSTNAME: ?
SHELL: /bin/bash
PWD: /home/bioinf/bioinf_data/57_boge/Erwinia_tasmaniensis/Genomes/seti_Erwinia_tasmaniensis_54G
PATH: /home/bioinf/mambaforge/envs/bakta/bin:/home/bioinf/mambaforge/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
Progam name:  amrfinder
Command line: amrfinder -u

Still,curl can access the available URL:

curl https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
<html>
 <head>
  <title>Index of /pathogen/Antimicrobial_resistance/AMRFinderPlus/database</title>
 </head>
 <body>
<h1>Index of /pathogen/Antimicrobial_resistance/AMRFinderPlus/database</h1>
<pre>Name                                              Last modified      Size  <hr><a href="/pathogen/Antimicrobial_resistance/AMRFinderPlus/">Parent Directory</a>                                                       -   
<a href="3.10/">3.10/</a>                                             2021-12-22 13:07    -   
<a href="3.2/">3.2/</a>                                              2019-10-31 11:24    -   
<a href="3.6/">3.6/</a>                                              2020-03-25 08:36    -   
<a href="3.8/">3.8/</a>                                              2020-10-02 15:43    -   
<a href="3.9/">3.9/</a>                                              2020-12-21 10:09    -   
<a href="3.10/">3.10/</a>                                              2022-10-12 10:00    -
<a href="3.11/">3.11/</a>                                              2022-10-12 10:00    -
<a href="latest/">latest/</a>                                             2021-12-22 13:19    -   
<hr></pre>

For now, I manually dowloaded the databases and formatted them with 'amrfinder_index' as suggested, and it runs fine when pointing to the database using '-d', thanks a lot.

Still, it would be good to know why 'amrfinder_update' is not working, since I am trying to use AMRfinder wrapped in 'bakta', and I cannot point to the appropriate database there.

I suspect there is a problem with proxy certificates, since the conda recipe installs its own version of 'curl' and 'openssl'. Setting this ip inside a conda environment is beyond my expertise though.

evolarjun · 2023-05-05T15:36:59Z

Thanks for the report. We haven't, so far, been able to replicate the issue, but we're trying to figure out what could be going on with this. There appears to be something different about the what libcurl is doing when called by AMRFinderPlus and what the command-line curl is doing, but we haven't figured anything out yet. We'll look into it and hopefully find something.

You're the second person we've heard having trouble with updates from within BAKTA. I don't think it's something BAKTA-specific, but as you suggest it could also be bioconda-related.

Do you know if you're running a version of command-line curl installed with bioconda?

Thanks again for your report, we're still trying to figure it out.

vbrover · 2023-05-06T17:13:17Z

Was your amrfinder_update or amrfinder -u successful on the same computer in the past?
Is your amrfinder_update or amrfinder -u successful on a different computer?

AMRFinderPlus release 3.11.14 This release addresses a few issues brought up on GitHub. We weren't able to solve all of them when we couldn't reproduce them, but we are trying. Changes: - On failure no `-o` output file is created - #115 - AMRFinderPlus will now automatically decompress files ending in .gz with gunzip (relies on gunzip being in PATH) - #61 - AMRFinderPlus does not support unicode, but it no longer checks GFF files to prohibit unicode characters specifically - #119 - Add reporting of curl error messages - #120

vbrover · 2023-05-10T14:27:07Z

Please try the newly released amrfinder ver. 3.11.14 which will print cURL error messages.

This release addresses a few issues brought up on GitHub. Changes: - On failure no `-o` output file is created - ncbi/amr#115 - AMRFinderPlus will now automatically decompress files ending in .gz with gunzip (this relies on gunzip being in PATH) - ncbi/amr#61 - AMRFinderPlus does not support unicode, but it will not check GFF files to prohibit extended ASCII or UTF-8 characters specifically (still prohibits GFF files with ASCII control characters 0x00 and 0x1F) - ncbi/amr#119 - Add reporting of curl error messages - ncbi/amr#120

ireneortega · 2024-01-23T12:20:58Z

I got the same error:

(campype) campype@campype-VirtualBox:~/CamPype$ amrfinder --update
Running: amrfinder --update
Software directory: '/home/campype/anaconda3/envs/campype/bin/'
Software version: 3.11.2
The number of threads cannot be greater than 1 on this computer
The current number of threads is 4, reducing to 1
Running: /home/campype/anaconda3/envs/campype/bin/amrfinder_update -d /home/campype/anaconda3/envs/campype/share/amrfinderplus/data
Looking up the published databases at https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/
 

*** ERROR ***
CURL: Cannot read from https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/

HOSTNAME: ?
SHELL: /bin/bash
PWD: /home/campype/CamPype
PATH: /home/campype/anaconda3/envs/campype/bin:/home/campype/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin
Progam name:  amrfinder_update
Command line: /home/campype/anaconda3/envs/campype/bin/amrfinder_update -d /home/campype/anaconda3/envs/campype/share/amrfinderplus/data
 
*** ERROR ***
'/home/campype/anaconda3/envs/campype/bin/amrfinder_update'  -d '/home/campype/anaconda3/envs/campype/share/amrfinderplus/data' > /tmp/amrfinder.ujBNZb/log
status = 256
 
 
HOSTNAME: ?
SHELL: /bin/bash
PWD: /home/campype/CamPype
PATH: /home/campype/anaconda3/envs/campype/bin:/home/campype/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin
Progam name:  amrfinder
Command line: amrfinder --update

What can I do?

vbrover · 2024-01-23T15:01:10Z

Can you connect to

https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/

from your browser on the computer where amrfinder is run?
(Or using wget or curl etc.)

vbrover · 2024-01-23T15:03:15Z

Also it would be better to use the most recent available version (3.11.26) of amrfinder.

evolarjun added bug Something isn't working can't reproduce Bug or apparent bug that we can't yet reproduce labels May 9, 2023

evolarjun mentioned this issue May 10, 2023

Release 3.11.14 #122

Merged

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amrfinder_update cannot connect to FTP and thus download #bug #help #120

amrfinder_update cannot connect to FTP and thus download #bug #help #120

geboro commented May 4, 2023

vbrover commented May 4, 2023

vbrover commented May 4, 2023

vbrover commented May 4, 2023

evolarjun commented May 4, 2023

geboro commented May 5, 2023

evolarjun commented May 5, 2023

vbrover commented May 6, 2023

vbrover commented May 10, 2023

ireneortega commented Jan 23, 2024

vbrover commented Jan 23, 2024 •

edited

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vbrover commented Jan 23, 2024

amrfinder_update cannot connect to FTP and thus download #bug #help #120

amrfinder_update cannot connect to FTP and thus download #bug #help #120

Comments

geboro commented May 4, 2023

vbrover commented May 4, 2023

vbrover commented May 4, 2023

vbrover commented May 4, 2023

evolarjun commented May 4, 2023

geboro commented May 5, 2023

evolarjun commented May 5, 2023

vbrover commented May 6, 2023

vbrover commented May 10, 2023

ireneortega commented Jan 23, 2024

vbrover commented Jan 23, 2024 • edited Loading

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