Manifest does not exist error

Technical Support
1

Dear Matthew,

Thank you for your response.
I have imported data in qiime2. It has demux.qza file was generated. File name is demux.qza

When I run second command to check quality of data. Error comes. Please, see command and error appered.

It is:
time qiime demux summarize
–i-data demux.qza
–o-visualization demux.qzv

Plugin error from demux:

[Errno 2] File b’/var/folders/1f/dgymh0l92xz6q91mqt0l2y800000gn/T/qiime2-archive-x9_doten/84a61338-9fc6-49e8-93e8-2204e040874b/data/MANIFEST’ does not exist: b’/var/folders/1f/dgymh0l92xz6q91mqt0l2y800000gn/T/qiime2-archive-x9_doten/84a61338-9fc6-49e8-93e8-2204e040874b/data/MANIFEST’

Debug info has been saved to /var/folders/1f/dgymh0l92xz6q91mqt0l2y800000gn/T/qiime2-q2cli-err-no_m0z3y.log

real 0m9.396s

user 0m6.437s

sys 0m0.920s

2

Can you please run the following:

qiime tools validate demux.qza

and paste the results here?

Thanks! :qiime2:

3

Hi,
Thank you for sharing command. Here is terminal output.

Last login: Wed Jul 10 08:30:49 on ttys001

(base) Bhagwans-MacBook-Pro:desktop rekadwad$ conda activate qiime2-2019.4

(qiime2-2019.4) Bhagwans-MacBook-Pro:desktop rekadwad$ ls

Call letter.pdf MiSeq SOP - mothur.pdf Terminal Saved Output2 mothur

Metadata.tsv Terminal Saved Output1 demux.qza sequence_data

(qiime2-2019.4) Bhagwans-MacBook-Pro:desktop rekadwad$ qiime tools validate demux.qza

Result demux.qza appears to be valid at level=max.

(qiime2-2019.4) Bhagwans-MacBook-Pro:desktop rekadwad$

4

Can you provide more information about the system you are attempting to run this command on? Thanks!

5

Dear Matthew,
Here is the information of my system.

MacBook Pro (13-inch, early 2011), processor 2.7 GHz, Intel Core i7, RAM 16 GB 1333 MHz DDR3, Gaphics: Intel HD Graphics 3000 512 MB, HDD: 750 GB.

Thank you.

6

Have you tried running the command again? Any chance it was just a transient issue? Maybe try again without running the time command.

7

Hi,
I tried it many times. But, I am getting same error.
Please see error appeared again.

(qiime2-2019.4) Bhagwans-MacBook-Pro:~ rekadwad$ cd desktop

(qiime2-2019.4) Bhagwans-MacBook-Pro:desktop rekadwad$ qiime demux summarize --p-n 10000 --i-data demux.qza --o-visualization qual_viz

Plugin error from demux:

[Errno 2] File b'/var/folders/1f/dgymh0l92xz6q91mqt0l2y800000gn/T/qiime2-archive-gdlbtzat/f6af3b04-80ac-4bc2-9583-1748b05b6bf1/data/MANIFEST' does not exist: b'/var/folders/1f/dgymh0l92xz6q91mqt0l2y800000gn/T/qiime2-archive-gdlbtzat/f6af3b04-80ac-4bc2-9583-1748b05b6bf1/data/MANIFEST'

Debug info has been saved to /var/folders/1f/dgymh0l92xz6q91mqt0l2y800000gn/T/qiime2-q2cli-err-65amx5up.log

AND second time other way

(qiime2-2019.4) Bhagwans-MacBook-Pro:desktop rekadwad$ qiime demux summarize \

--i-data demux.qza \

--o-visualization demux.qzv

Plugin error from demux:

[Errno 2] File b'/var/folders/1f/dgymh0l92xz6q91mqt0l2y800000gn/T/qiime2-archive-78hd1qgf/f6af3b04-80ac-4bc2-9583-1748b05b6bf1/data/MANIFEST' does not exist: b'/var/folders/1f/dgymh0l92xz6q91mqt0l2y800000gn/T/qiime2-archive-78hd1qgf/f6af3b04-80ac-4bc2-9583-1748b05b6bf1/data/MANIFEST'

Debug info has been saved to /var/folders/1f/dgymh0l92xz6q91mqt0l2y800000gn/T/qiime2-q2cli-err-yl3yczgl.log

I am getting same error.

Is there any problem with MANIFEST file and metadata.yml file?
If yes, please share MANIFEST file and metadata.yml file formats.

Please suggest.

8

Please provide us with a download link to your data file demux.qza. Thanks!

9

Hi,
Here is link for demux.qza file: https://drive.google.com/file/d/1zvu8GU3WAkEJJy89zPum1d5I3Y7_X_2O/view?usp=sharing

Thank you.

10

Thanks for sharing @Bhagwan! It looks like you imported this by manually creating a SingleLanePerSamplePairedEndFastqDirFmt format, which is really impressive! Unfortunately, it looks like things went wrong, which isn’t surprising — this format is not really designed for people to create, but rather, for computers. Judging by your filenames, it would be easiest to use one of the Casava import formats.

Please give that a try and let us know how it goes.

1 Like
11

Thank you @thermokars -Matthew Ryan Dillon.
Yep. I have good news. It’s working. I am learning qiime2. I will ask you for help if I stuck somewhere. Thank you once again.

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