Importing manifest.tsv

Technical Support
1

I have made my meta-data, and manifest and validated them. Iv saved visualization. I used the command LS and it shows my sample I'd, forward - absolute - filepath
Reverse-absolute-filepath and then my samples. When I am typing the command
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path manifest.2tsv
--output-path paired-end-demux. qza
--input-format PairedEndFastaqManifestPhred33v2

I get an error
There is a problem importing Manifest 2. tsv

manifest2. Tsv is not a (n) PairedEndManifestPhred33v2 file
And

Filepath on line 1 and colum "forward-absoluts-filepath" could not be found for "Sample-1"

Can anyone help

2

Could u share the tsv?

1 Like
3

There is a typo here, it should be "forward-absolute-filepath" (note the s->e in "absolute").

Edit, just realized that you manually wrote out the error message (in the future please copy and paste). Ignore the typo suggestion above. The actual error is that your forward read for "Sample-1" couldn't be found - that means there is a typo in the filepath you have provided. Please carefully double-check.

1 Like
4

I have rewritten the manifest - I have tried both of these commands,qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path manifest3.tsv
--output-path paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2

qiime tools import
--type "SampleData[SequencesWithQuality]"
--input-format PairedEndFastqManifestPhred33V2
--input-path ./manifest3.tsv
--output-path ./demux_seq.qza

My $ completely disappears and the nothing happens. I try to log out and start again but the same things occurs and cant even change directory

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5

My $ completely disappears and the nothing happens.

How many samples do you work with? You might be being impatient.

Also, just like @Francisco said, could you share manifest file?

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6

agree with @the_dummy I would wait until you get the prompt again, but yeah, I'd like to see at least a screenshot of the manifest! Ben

7

I think i have done it.
My internet on the mountains is so slow- it took hours to complete the 15 samples.
Thanks for all your help.
I am now in the process of denoising. Looking at my visuals its pretty good

image
image1366×768 84.8 KB

what parameters should i set for this? I have used the deblurr but re-runnig with dada2 as the tutorial only includes info from the dada.

1 Like
8

Please resubmit this question as a new topic post --- this will help keep things searchable and easy-to-follow for others here on the forum.

11

Quick question, as an aside, what does your internet connection have to do with the creation of the demux? Are you running the samples from a HPC? Ben

12

6 posts were split to a new topic: Manifest Errors Issues

13

7 posts were split to a new topic: I have a problem in importing the data using manifest