Error msg from importing the data with the manifest csv,

Technical Support
1

Hi So I haved tried multiple things to get it right but for some reason, it does not work... witht he error msg that i do not know what to do.

(qiime2-2019.4) Jiyoungs-MacBook-Pro:Vagus_fastq Sammy$ qiime tools import --type 'SampleData[JoinedSequencesWithQuality]' --input-path 16Smanifest.csv --output-path manifest.qza --input-format SingleEndFastqManifestPhred33

There was a problem importing 16Smanifest.csv:

16Smanifest.csv is not a(n) SingleEndFastqManifestPhred33 file:

Found header on line 1 with the following labels: ['sample_id', 'absolute-filepath', 'direction', 'sampleType', 'treatment', 'feces_id'], expected: ['sample-id', 'absolute-filepath', 'direction']

I have changed my manifest.csv and validated with keemi but it still does give me the error msg... is there anyone who could help me?

Also, the files are merged files (fastq) but treated as single-endfastq for importing it.

2

Hi @Sammi!
I don't have a ton of experience with this import format, but you may have too many columns in your header. As the error message says, the command expects:

Perhaps you are using a complete metadata file, instead of the simpler manifest format?
Try cutting the extra columns out of your manifest, saving, and re-running. If that give you trouble, let us know!

Chris

p.s. When/if you want to try something different, the new (V2) manifest format is pretty snazzy :confetti_ball::man_dancing::dancer::sparkler:. You can find all the details in the importing tutorial.

3

Thank you Chris!

So I did try the simpler ver. of the manifest file only with sample id, path, direction.

And I got this.
There was a problem importing 16Smanifest1.csv:

16Smanifest1.csv is not a(n) SingleEndFastqManifestPhred33 file:

Found header on line 1 with the following labels: ['sample_id', 'absolute-filepath', 'direction'], expected: ['sample-id', 'absolute-filepath', 'direction']

So I am very confused...?

4

Ah, you have an underscore for sample_id, but it expects a dash sample-id.

2 Likes
5

Thank you that was the problem!
And Now I am having another trouble but i think i can handle it! :slight_smile:

6

So follow up with this, I get another problem which it says

(qiime2-2019.4) Jiyoungs-MacBook-Pro:Vagus_fastq Sammy$ qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path 16Smanifest_TJK.csv --output-path manifest.qza --input-format SingleEndFastqManifestPhred33

There was a problem importing 16Smanifest_TJK.csv:

16Smanifest_TJK.csv is not a(n) SingleEndFastqManifestPhred33 file:

File referenced on line 29 could not be found (/Users/Sammy/Desktop/Vagus_fastq/vagus_fastq/BHF7.fastq).

I doubled checked where my fastq file path is... and copied and pasted on my manifest file.. so I am very confused what to do and i think, it might be something to do with our fastq file itself?

7

Can you please run the following command and share the results?

ls /Users/Sammy/Desktop/Vagus_fastq/vagus_fastq/BHF7.fastq
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ls: /Users/Sammy/Desktop/Vagus_fastq/vagus_fastq/BHF7.fastq: No such file or directory

This is what i get when i ran the command... I dont understand it, the file is in the folder though?

9

Hi @Sammi! Please double-check the spelling and location of the file --- ls isn't lying when it says it can't find that file exactly as specified. Maybe you could share a screenshot of the folder with your sequences in it?

1 Like
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A post was split to a new topic: Invalid metadata