q2-fondue: sra-tools configuration

Technical Support
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I've download all of the run IDs of the dataset of the moshpit tutorial, using the default code with my e-mail address, but only changed the code with "--p-threads 11", but every run ID need to experience seven times of "Failed to download sequences. Error: This sra toolkit installation has not been configured". How to avoid these errers, and download at once?

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After the process above, I've achieved the next step with:

 mosh demux summarize \
    --i-data ./cache:reads_paired \
    --o-visualization demux.qzv

And also achieved it with replacing the "reads_paired" with "reads_single", however neither of theirs information could be viewed by the website after run "qiime tools view demux.qzv". So, I guess I've not really download the run IDs.

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What's wrong with my operations?
By the way, I think it is not easy to show the results of the generated "qzv" files, opposite to deal with Amplicon data under VirtualBox-Linux environment as before. In the past, it could be shown directly after run the viewing code, but now the local website appears at the first, and then it should be copied and paste in an internet explore, finally we can see the result.

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Did you read the next line in the output?
(It tells you exactly what to do. So try that and report back here.)

They also give you a link to their docs, so go read those too.

2 Likes
3

I‘ve used command "vdb-config -i", and change the settings with directions from "03. Quick Toolkit Configuration · ncbi/sra-tools Wiki · GitHub", but there is another warning appeared: "FutureWarning: DataFrame.groupby with axis=1 is deprecated. Do frame.T.groupby(...) without axis instead.
df = df.groupby(level=0, axis=1).first()". The download was so slowly (one ID needs spend 30+minutes, so I stop the running), I think this warning should be resolved, how to do that?

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Then, I run the same command again, it show same warning, but not same as before, the download was processing, and another errror appeared: "Fetching failed. Error: fasterq-dump quit with error code 3", and nothing had been downloaded, so I break the process again.
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1 Like
4

Hi @yangyue ,
A FutureWarning is only a warning, about code that will need to be changed due to future changes to another software package used by this action. So this does not need to be changed now, and will not impact the functionality at this time.

The process is slow because you are downloading metagenome sequence data, and depending on location and local network connection etc the time to download could vary. The fact that it is taking time is a good indication that this step is now working. So I recommend just being patient with this step.

Good luck!

1 Like
5

Thank you. As you say, I run the same command again, but there had another question as I described before your reply.
I write down the error situation and added it after the warning I've described before your reply.

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I suspect this could be a firewall issue, unless if it is an issue with that one sample (it is impossible to tell because you canceled that job)

1 Like
8

Thank you！
I‘ve kept firewall and turned off firewall, and run the code again, both of these situations show "cannot find 'SRR9640350' -> RC(rcVFS,rcQuery,rcResolving,rcName,rcNotFound) fasterq-dump quit with error code 3", and nothing has been download.

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(turned off firewall)

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Hey @yangyue,

can it be that the machine/laptop you are running this from is behind a proxy? If that's the case you may need to configure that in addition (GitHub - bokulich-lab/q2-fondue: Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere).

3 Likes
10

Thank you！I have some local data, so the sentence "mosh fondue get-all" may not fittable for my current working, I prefer to use "mosh fondue combine-seqs" in future.