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
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
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
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.
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:
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.
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. Hereβs what I've done so far:
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%|βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ| 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%|βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ| 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%|βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ| 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%|βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ| 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
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
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.