error installing q2-fondue in version 2024.5

I followed the steps to activate the environment (Macbook pro-M3 chip)
(base) srinivasanmahalingam@mwc-202239 ~ % conda activate qiime2-amplicon-2024.2
(qiime2-amplicon-2024.2) srinivasanmahalingam@mwc-202239 ~ % mamba install -y
-c https://packages.qiime2.org/qiime2/amplicon-2024.2 /tested/
-c conda-forge -c bioconda -c defaults
q2-fondue

usage: mamba [-h] [-v] [--no-plugins] [-V] COMMAND ...
mamba: error: unrecognized arguments: q2-fondue

Hi @MSrinivasan!
Your command looks good except for the extra space between '2024.2' and '/tested/' in the packages link.

Please try removing that space and then re running the command.
if that doesn't work please post your entire command and the entire error message output here and we can troubleshoot it from there.
--Hannah

Thank you Hannah,
I tried but its not working!

here you go the new commends
I updated new version: (qiime2-amplicon-2024.5)

(qiime2-amplicon-2024.5) srinivasanmahalingam@mwc-202239 ~ % mamba install -y
-c https://packages.qiime2.org/qiime2/amplicon-2024.5/tested/
-c conda-forge -c bioconda -c defaults
q2-fondue

Looking for: ['q2-fondue']

https://packages.qiime2.org/qiime2/amplicon-2024.. 0.2s
https://packages.qiime2.org/qiime2/amplicon-2024.. Checked 0.1s
warning libmamba Cache file "/Users/srinivasanmahalingam/miniforge3/pkgs/cache/31ce02e0.json" was modified by another program
conda-forge/noarch Using cache
warning libmamba Cache file "/Users/srinivasanmahalingam/miniforge3/pkgs/cache/35adf087.json" was modified by another program
bioconda/osx-64 (check zst) Checked 0.1s
bioconda/noarch Using cache
warning libmamba Cache file "/Users/srinivasanmahalingam/miniforge3/pkgs/cache/7fb2ce72.json" was modified by another program
pkgs/main/osx-64 (check zst) Checked 0.1s
warning libmamba Cache file "/Users/srinivasanmahalingam/miniforge3/pkgs/cache/dd44a73b.json" was modified by another program
pkgs/r/osx-64 (check zst) Checked 0.0s
https://packages.qiime2.org/qiime2/amplicon-2024.. 153.0 B @ 2.8kB/s 404 failed 0.1s
pkgs/main/noarch No change
https://packages.qiime2.org/qiime2/amplicon-2024.. 404 failed 0.3s
Multi-download failed. Reason: Transfer finalized, status: 404 [https://packages.qiime2.org/qiime2/amplicon-2024.5/tested/noarch/repodata.json] 153 bytes

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/Users/srinivasanmahalingam/miniforge3/lib/python3.10/site-packages/conda/exception_handler.py", line 18, in __call__
    return func(*args, **kwargs)
  File "/Users/srinivasanmahalingam/miniforge3/lib/python3.10/site-packages/mamba/mamba.py", line 959, in exception_converter
    raise e
  File "/Users/srinivasanmahalingam/miniforge3/lib/python3.10/site-packages/mamba/mamba.py", line 952, in exception_converter
    exit_code = _wrapped_main(*args, **kwargs)
  File "/Users/srinivasanmahalingam/miniforge3/lib/python3.10/site-packages/mamba/mamba.py", line 898, in _wrapped_main
    result = do_call(parsed_args, p)
  File "/Users/srinivasanmahalingam/miniforge3/lib/python3.10/site-packages/mamba/mamba.py", line 763, in do_call
    exit_code = install(args, parser, "install")
  File "/Users/srinivasanmahalingam/miniforge3/lib/python3.10/site-packages/mamba/mamba.py", line 469, in install
    index = load_channels(pool, channels, repos)
  File "/Users/srinivasanmahalingam/miniforge3/lib/python3.10/site-packages/mamba/utils.py", line 126, in load_channels
    index = get_index(
  File "/Users/srinivasanmahalingam/miniforge3/lib/python3.10/site-packages/mamba/utils.py", line 107, in get_index
    is_downloaded = dlist.download(api.MAMBA_DOWNLOAD_FAILFAST)
RuntimeError: Multi-download failed. Reason: Transfer finalized, status: 404 [https://packages.qiime2.org/qiime2/amplicon-2024.5/tested/noarch/repodata.json] 153 bytes

$ /Users/srinivasanmahalingam/miniforge3/bin/mamba install -y -c https://packages.qiime2.org/qiime2/amplicon-2024.5/tested/ -c conda-forge -c bioconda -c defaults q2-fondue

environment variables:
CIO_TEST=
CMAKE_PREFIX_PATH=:/Users/srinivasanmahalingam/miniforge3/envs/qiime2-amplicon-2024.5
CONDA_BACKUP_HOST=mwc-202239.dhcp.missouri.edu
CONDA_DEFAULT_ENV=qiime2-amplicon-2024.5
CONDA_EXE=/Users/srinivasanmahalingam/miniforge3/bin/conda
CONDA_PREFIX=/Users/srinivasanmahalingam/miniforge3/envs/qiime2-amplicon-2024.5
CONDA_PREFIX_1=/Users/srinivasanmahalingam/miniforge3
CONDA_PROMPT_MODIFIER=(qiime2-amplicon-2024.5)
CONDA_PYTHON_EXE=/Users/srinivasanmahalingam/miniforge3/bin/python
CONDA_ROOT=/Users/srinivasanmahalingam/miniforge3
CONDA_SHLVL=2
CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0
CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0
CURL_CA_BUNDLE=
JAVA_LD_LIBRARY_PATH=/Users/srinivasanmahalingam/miniforge3/envs/qiime2-amplicon-
2024.5/lib/jvm/lib/server
LD_PRELOAD=
PATH=/Users/srinivasanmahalingam/miniforge3/envs/qiime2-amplicon-
2024.5/bin:/Users/srinivasanmahalingam/miniforge3/condabin:/usr/local/
bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/r
un/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/v
ar/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var
/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinter
nal/bin
PYTHONNOUSERSITE=/Users/srinivasanmahalingam/miniforge3/envs/qiime2-amplicon-
2024.5/lib/python*/site-packages/
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=

 active environment : qiime2-amplicon-2024.5
active env location : /Users/srinivasanmahalingam/miniforge3/envs/qiime2-amplicon-2024.5
        shell level : 2
   user config file : /Users/srinivasanmahalingam/.condarc

populated config files : /Users/srinivasanmahalingam/miniforge3/.condarc
/Users/srinivasanmahalingam/.condarc
/Users/srinivasanmahalingam/miniforge3/envs/qiime2-amplicon-2024.5/.condarc
conda version : 24.5.0
conda-build version : not installed
python version : 3.10.14.final.0
solver : libmamba (default)
virtual packages : __archspec=1=x86_64
__conda=24.5.0=0
__osx=14.5=0
__unix=0=0
base environment : /Users/srinivasanmahalingam/miniforge3 (writable)
conda av data dir : /Users/srinivasanmahalingam/miniforge3/etc/conda
conda av metadata url : None
channel URLs : https://packages.qiime2.org/qiime2/amplicon-2024.5/tested/osx-64
https://packages.qiime2.org/qiime2/amplicon-2024.5/tested/noarch
conda-forge/osx-64
conda-forge/noarch
bioconda/osx-64
bioconda/noarch
main/osx-64
main/noarch
r/osx-64
r/noarch
package cache : /Users/srinivasanmahalingam/miniforge3/pkgs
/Users/srinivasanmahalingam/.conda/pkgs
envs directories : /Users/srinivasanmahalingam/miniforge3/envs
/Users/srinivasanmahalingam/.conda/envs
platform : osx-64
user-agent : conda/24.5.0 requests/2.31.0 CPython/3.10.14 Darwin/23.5.0 OSX/14.5 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8
UID:GID : 501:20
netrc file : None
offline mode : False

An unexpected error has occurred. Conda has prepared the above report.
If you suspect this error is being caused by a malfunctioning plugin,
consider using the --no-plugins option to turn off plugins.

Example: conda --no-plugins install

Alternatively, you can set the CONDA_NO_PLUGINS environment variable on
the command line to run the command without plugins enabled.

Example: CONDA_NO_PLUGINS=true conda install

Hi @MSrinivasan,
Turns out that the commands are currently being updated for the latest release! and explains why the commands you were used were not functioning properly. We can definitely get it working! I have a few questions so I can help you get the right environment:
What kind of analysis are you hoping to do? are you doing a metagenomic workflow or a 16s amplicon analysis?
if you are working with metagenomic data I would recommend installing the metagenomic distribution which conveniently comes with the q2-fondue plugin!
Otherwise the commands to add q2-fondue to a 2024.5 amplicon environment are:

mamba install -y \
-c https://packages.qiime2.org/qiime2/2024.5/metagenome/released/ \
-c conda-forge -c bioconda -c defaults \
q2-fondue

Let me know if you have any further questions :slight_smile:
--Hannah

1 Like

Hi Hannah,

Thanks for the update and the instructions! I am working with QIIME 2 for 16s amplicon analysis. I appreciate the guidance on installing q2-fondue.

I will proceed with the installation using the provided commands. If I encounter any issues or have further questions during the process, I will let you know.

Thanks again for your assistance!

Best regards, @MSrinivasan

2 Likes

Trouble with Qiime2 fondue Plugin: Sequence Download Issue
Hi,

I'm encountering an issue with Qiime2's fondue plugin while trying to download sequences from NCBI using accession IDs. Here’s what I've done so far:

  1. Imported accession IDs successfully using:
    qiime tools import
    --type NCBIAccessionIDs
    --input-path metadata_file_runs.tsv
    --output-path metadata_file_runs.qza

  2. Attempted to fetch sequences with the get-all command:

qiime fondue get-all
--i-accession-ids metadata_file_runs.qza
--p-email mahasiva2@gmail.com
--p-retries 3
--verbose
--output-dir fondue-output

However, I encountered errors where most sequences failed to download. I then tried fetching the failed IDs individually using:
qiime fondue get-sequences
--i-accession-ids fondue-output/failed_runs.qza
--p-email mahasiva2@gmail.com
--o-single-reads refetched_single
--o-paired-reads refetched_paired
--o-failed-runs refetched_failed

But I received a plugin error stating that neither single- nor paired-end sequences could be downloaded. I have verified the accession IDs and my email address, and I'm unsure where the issue lies.

Any suggestions or insights would be greatly appreciated.

Thank you!

*** I run the qiime tools import
--type NCBIAccessionIDs
--input-path metadata_file_runs.tsv
--output-path metadata_file_runs.qza no error then i followed (qiime2-amplicon-2024.5) srinivasanmahalingam@mwc-201104 ~ % qiime fondue get-all
--i-accession-ids metadata_file_runs.qza
--p-email mahasiva2@gmail.com
--p-retries 3
--verbose
--output-dir fondue-output 2024-06-20 12:41:40,165 [MainThread] [INFO] [entrezpy.esearch.esearcher.Esearcher]: {"query": "_-mNq6IPRcOqbM-cNiFyrA==", "status": "OK"} 2024-06-20 12:41:40,251 [MainThread] [INFO] [q2_fondue.metadata]: Fetching metadata for 28 run IDs. /Users/srinivasanmahalingam/miniforge3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_fondue/entrezpy_clients/_efetch.py:69: FutureWarning: DataFrame.groupby with axis=1 is deprecated. Do frame.T.groupby(...) without axis instead. df = df.groupby(level=0, axis=1).first() 2024-06-20 12:41:43,469 [MainThread] [INFO] [q2_fondue.sequences]: Downloading sequences for 28 accession IDs... Downloading sequences for run SRR19667910 (attempt 1): 100%|β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆ| 28/28 [03:45<00:00, 8.06s/it, 27 failed] 2024-06-20 12:45:29,048 [MainThread] [INFO] [q2_fondue.sequences]: Retrying to download the following failed accession IDs in 0.8 min: ['SRR19667815', 'SRR19667826', 'SRR19667837', 'SRR19667851', 'SRR19667858', 'SRR19667870', 'SRR19667881', 'SRR19667884', 'SRR19667885', 'SRR19667886', 'SRR19667887', 'SRR19667888', 'SRR19667889', 'SRR19667890', 'SRR19667891', 'SRR19667892', 'SRR19667893', 'SRR19667894', 'SRR19667895', 'SRR19667896', 'SRR19667897', 'SRR19667898', 'SRR19667899', 'SRR19667900', 'SRR19667901', 'SRR19667908', 'SRR19667909'] Downloading sequences for run SRR19667909 (attempt 2): 100%|β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆ| 27/27 [01:46<00:00, 3.95s/it, 27 failed] 2024-06-20 12:48:00,690 [MainThread] [INFO] [q2_fondue.sequences]: Retrying to download the following failed accession IDs in 1.0 min: ['SRR19667815', 'SRR19667826', 'SRR19667837', 'SRR19667851', 'SRR19667858', 'SRR19667870', 'SRR19667881', 'SRR19667884', 'SRR19667885', 'SRR19667886', 'SRR19667887', 'SRR19667888', 'SRR19667889', 'SRR19667890', 'SRR19667891', 'SRR19667892', 'SRR19667893', 'SRR19667894', 'SRR19667895', 'SRR19667896', 'SRR19667897', 'SRR19667898', 'SRR19667899', 'SRR19667900', 'SRR19667901', 'SRR19667908', 'SRR19667909'] Downloading sequences for run SRR19667909 (attempt 3): 100%|β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆ| 27/27 [01:51<00:00, 4.14s/it, 27 failed] 2024-06-20 12:50:52,577 [MainThread] [INFO] [q2_fondue.sequences]: Retrying to download the following failed accession IDs in 1.5 min: ['SRR19667815', 'SRR19667826', 'SRR19667837', 'SRR19667851', 'SRR19667858', 'SRR19667870', 'SRR19667881', 'SRR19667884', 'SRR19667885', 'SRR19667886', 'SRR19667887', 'SRR19667888', 'SRR19667889', 'SRR19667890', 'SRR19667891', 'SRR19667892', 'SRR19667893', 'SRR19667894', 'SRR19667895', 'SRR19667896', 'SRR19667897', 'SRR19667898', 'SRR19667899', 'SRR19667900', 'SRR19667901', 'SRR19667908', 'SRR19667909'] Downloading sequences for run SRR19667909 (attempt 4): 100%|β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆ| 27/27 [01:54<00:00, 4.26s/it, 27 failed] 2024-06-20 12:54:17,561 [MainThread] [INFO] [q2_fondue.sequences]: Download finished. 27 out of 28 runs failed to fetch. Below are the error messages of the first 5 failed runs: ID=SRR19667815, Error=fasterq-dump quit with error code 3

ID=SRR19667826, Error=fasterq-dump quit with error code 3

ID=SRR19667837, Error=fasterq-dump quit with error code 3

ID=SRR19667851, Error=fasterq-dump quit with error code 3

ID=SRR19667858, Error=fasterq-dump quit with error code 3

2024-06-20 12:54:17,581 [MainThread] [WARNING] [q2_fondue.sequences]: No single-end sequences available for these accession IDs. 2024-06-20 12:54:17,593 [MainThread] [INFO] [q2_fondue.sequences]: Processing finished. Saved SRAMetadata to: fondue-output/metadata.qza Saved SampleData[SequencesWithQuality] to: fondue-output/single_reads.qza Saved SampleData[PairedEndSequencesWithQuality] to: fondue-output/paired_reads.qza Saved SRAFailedIDs to: fondue-output/failed_runs.qza

Then i tried

fondue-output/failed_runs.qza (qiime2-amplicon-2024.5) srinivasanmahalingam@mwc-201104 ~ % qiime fondue get-sequences
--i-accession-ids fondue-output/failed_runs.qza \ --p-email mahasiva2@gmail.com
--o-single-reads refetched_single
--o-paired-reads refetched_paired
--o-failed-runs refetched_failed Plugin error from fondue:

Neither single- nor paired-end sequences could be downloaded. Please check your accession IDs.

Debug info has been saved to /var/folders/gx/9zlbmhs13qj0ws5sbbjrxyfh0000gn/T/qiime2-q2cli-err-9a2z_d9a.log***

Hi @MSrinivasan,
I looked into this error and it says that its typically a storage issue

Have you run the vdb-config command to configure the SRA tool-kit?

The command is:

vdb-config -i

more information can be found here:

Hope this helps!
:turtle:

2 Likes

Thank you Cherman2, I did thrice but still i am getting same error anything i have to change on that?

Hi @MSrinivasan,
You shouldn't have to do anything, unless you are on a proxy server. Here is more info on configuring the SRA toolkit that you should review: 05. Toolkit Configuration Β· ncbi/sra-tools Wiki Β· GitHub
If you already run that command, I would recommend confirming that you have the storage necessary on your device for your downloads

1 Like

Hi @cherman2! Thank you again for your help. I've gone through the SRA Toolkit Configuration Guide.

  • Proxy Settings:
  • I checked the proxy settings using networksetup -getwebproxy Wi-Fi and found that the web proxy is not enabled (Enabled: No), and there is no server or port specified (Server:, Port: 0). Therefore, it seems my network doesn't require a proxy for general web access.
  • Storage Availability:
  • I have checked my device's storage, and it shows that I have 923.61 GB available out of 994.66 GB. This should be sufficient for handling large genomics datasets that the SRA Toolkit processes.
  • Should I proceed with configuring vdb-config based on the standard settings provided, or are there specific adjustments I should make given my network and storage situation?

I will attach a screenshot of my configuration settings for your reference.

Hi @MSrinivasan,
this all looks correct, if you aren't enabling a proxy server there isnt alot to do on this config.

You could try this: https://www.ncbi.nlm.nih.gov/Traces/study/ to confirm space requirements but I agree 900 GB should be enough

Have you looked up the accession numbers in the SRA website that you are trying to download to make sure they exist?

Hope this helps!
:turtle:

1 Like

Hi @cherman2! Yes, I did Ids are correct. I tried manually using prefetch.

Here you go...

2024-06-21T18:28:12 prefetch.3.0.0: Current preference is set to retrieve SRA Lite files with simplified base quality scores.

2024-06-21T18:28:13 prefetch.3.0.0: 1) 'SRR19667815.lite' is found locally

2024-06-21T18:28:13 prefetch.3.0.0: 'SRR19667815' has 0 unresolved dependencies

(qiime2-amplicon-2024.5) srinivasanmahalingam@mwc-201104 ~ % fastq-dump --split-files --outdir /path/to/output/directory SRR19667815.sra

2024-06-21T18:30:24 fastq-dump.3.0.0 err: directory unauthorized while creating directory within file system module - failed to initialize files

=============================================================

An error occurred during processing.

A report was generated into the file '/Users/srinivasanmahalingam/ncbi_error_report.txt'.

If the problem persists, you may consider sending the file

to 'sra-tools@ncbi.nlm.nih.gov' for assistance.

=============================================================

fastq-dump quit with error code 3

Can you post the context of this file?

Sure! @cherman2, Here you go..







/Users/srinivasanmahalingam




















<quality_type>raw_scores</quality_type>



/Users/srinivasanmahalingam/.ncbi/user-settings.mkfg
/Users/srinivasanmahalingam/miniforge3/envs/qiime2-amplicon-2024.5/bin/ncbi/certs.kfg
/Users/srinivasanmahalingam/miniforge3/envs/qiime2-amplicon-2024.5/bin/ncbi/default.kfg
/Users/srinivasanmahalingam/miniforge3/envs/qiime2-amplicon-2024.5/bin/ncbi/vdb-copy.kfg

"fastq-dump"
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"RELEASE"
"/Users/srinivasanmahalingam"
"x86_64-apple-darwin13.4.0"

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<NCBI_HOME>"/Users/srinivasanmahalingam/.ncbi"</NCBI_HOME>
<NCBI_SETTINGS>"/Users/srinivasanmahalingam/.ncbi/user-settings.mkfg"</NCBI_SETTINGS>
"mac"
"/Users/srinivasanmahalingam"
"srinivasanmahalingam"

<DO_NOT_REDACT>"CS_KEY,FLOW_CHARS,KEY_SEQUENCE,LINKER_SEQUENCE"</DO_NOT_REDACT>

"col,.seq,STATS,BASE_COUNT,HUFFMAN_TREE_POS,HUFFMAN_TREE_POS_SIZE,HUFFMAN_TREE_PRB,HUFFMAN_TREE_PRB_SIZE,HUFFMAN_TREE_SIG,HUFFMAN_TREE_SIG_SIZE,MSC454_CLIP_QUALITY_LEFT,MSC454_CLIP_QUALITY_RIGHT,MSC454_FLOW_CHARS,MSC454_KEY_SEQUENCE,NREADS,NUMBER_POS_CHANNELS,NUMBER_PRB_CHANNELS_1,NUMBER_PRB_COLUMNS,NUMBER_SIG_CHANNELS,PLATFORM,READ_0,READ_1,SPOT_COUNT"

<NCBI_SRA_ABI_tbl_v1_1>
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</NCBI_SRA_ABI_tbl_v1_1>
<NCBI_SRA_Illumina_tbl_v0a_1>
"sra/illumina.vschema"
"NCBI:SRA:Illumina:tbl:phred:v2"
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<INSDC_color_text>
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<INSDC_dna_text>
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</INSDC_dna_text>
<NCBI_qual4>
"-6"
</NCBI_qual4>
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<INSDC_SRA_read_type>"1"</INSDC_SRA_read_type>
<INSDC_quality_log_odds>"1"</INSDC_quality_log_odds>
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<VDB_CONFIG></VDB_CONFIG>
<VDB_ROOT></VDB_ROOT>

<credential_file></credential_file>
"default"


"false"


<credential_file></credential_file>



"false"
":0"




"64"
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"user-settings.mkfg"



<accept_aws_charges>"false"</accept_aws_charges>
<accept_gcp_charges>"false"</accept_gcp_charges>

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"ZR"




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<SDL.2>
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</SDL.2>









"."




"."




"."




"."




"."




"."



"."


"false"
"/Users/srinivasanmahalingam/ncbi"





"files"




"nannot"




"nannot"




"refseq"




"sra"





"sra"

"updated"




"sra"

"updated"



"wgs"



"/Users/srinivasanmahalingam/.prefetch_cache"





<quality_type>"raw_scores"</quality_type>


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<download_to_cache>"true"</download_to_cache>





"/Users/srinivasanmahalingam/miniforge3/envs/qiime2-amplicon-2024.5/bin"









Thank you so much! This is awesome