search

spholmes / F1000_workflow

43 stars 33 forks source link

link to mothur miseq development data not working #10

Closed cmsmoo closed 7 years ago

cmsmoo commented 7 years ago

The link to the data returns this message: "The requested URL /MiSeqDevelopmentData/StabilityNoMetaG.tar was not found on this server."

is there another way to get this data to run the workflow?

Thanks.

benjjneb commented 7 years ago

The mothur.org site has been down a lot lately, and it appears this file is currently a casualty.

Here is a dropbox link that should work for now: DELETED

padpadpadpad commented 7 years ago

This file downloads fine using download.file("https://www.dropbox.com/s/5ue8476y3dzvxx2/StabilityNoMetaG.tar?dl=0", destfile = file.path(miseq_path, "StabilityNoMetaG.tar"))

but when unpacking the .tar file it reports: Unrecognised archive format Error exit delated from previous errors Seems to be a problem with the file downloaded.

Looking at the file in Terminal file StabilityNoMetaG.tar HTML document text, ASCII text, with very long lines

Could the file link provided not be downloading correctly? Thanks

padpadpadpad commented 7 years ago

This works if you manually download the file from the link and do not use the code provided. Look forward to working through the workflow. Cheers Dan

krisrs1128 commented 7 years ago

@padpadpadpad I think if you change the end of the link to ?dl=1 then the code should work. The issue is that the file download won't trigger unless dl is set to 1.

padpadpadpad commented 7 years ago

Thanks @krisrs1128 will have a go. Are these files also the trimmed versions? As none of them are as long as in the tutorial?

krisrs1128 commented 7 years ago

Okay, let us know if you have any trouble. Also, remember to delete (or move) the MiSeq_SOP directory before rerunning, otherwise the if() won't evaluate, hadn't thought of that when I wrote earlier.

I'm actually not sure if they're trimmed -- @benjjneb should know though.

benjjneb commented 7 years ago

These are the untrimmed/unfiltered fastq files.

Please let us know if this file doesn't or does work for people. I had to recreate the .tar from individual files as I didn't have the original saved.

padpadpadpad commented 7 years ago

The downloads works but they are the trimmed files. Here is a file of some of the quality plots. They are already trimmed.

qual_plot.pdf

benjjneb commented 7 years ago

Unfortunately it looks like I may not have saved the raw data. I am requesting an update from the mothur team on alternative download locations, and will report back as soon as I hear something.

If anyone happens to have the original .tar file lying around, let me know!

For now, the file I uploaded can be used as is as long as you skip the filtering steps in the workflow.

benjjneb commented 7 years ago

The file is once again available from its mothur.org download location, so everything should work as expected again.

alitahir0 commented 6 years ago

I am trying to download "MiSeqDevelopmentData" from http://www.mothur.org, however, the website is currently down. Is there any other place to download this dataset? Thank you.