Stalled at import with manifest file not reading

User Support
1

I am running a small sample to test the functionality of my analysis. I opened a previous manifest file that worked. I even reran the import with the original manifest file and it works. I copied my new columns into that file and kept the same format, but it is telling me "found unrecognized ID column name “Sample-id, forward-absolute-filepath,reverse-absolute-filepath, Bodysite, etc”. Keemei never helps because it gives problems qiime2 does not care about.

2

Good afternoon! Welcome to Qiime 2 :qiime2:

The manifest file needs to be in exactly the right format. Qiime is pretty picky about that.

Would you be willing to post your manifest file so we can compare it to the examples in this tutorial?
https://docs.qiime2.org/2019.4/tutorials/importing/#fastq-manifest-formats

Thanks!
Colin

3

GSM-partial V1-V2.csv (13.0 KB) GSM-partial V1-V2.txt (12.7 KB) GSM-partial V1-V2 new try6.txt (783 Bytes)

I have attached the original and some I have tried since. I went to the tutorial and stripped it down and now it cannot find the files.

4

This is what I am using to import

qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path ‘/media/sf_Shared/GSM-partial V1-V2 new try6.txt’
–output-path paired-end-demux.qza
–input-format PairedEndFastqManifestPhred33V2

5

Hell Steven,

I think I’ve found the issue! When I open up these files in a text editor, I see this:

sample_name_with_underscores	'file/path/with/single/quotes/R1.fq.gz'

But the example shows this:

sample-name-with-dashes      file/path/withOUT/quotes/R1.fq.gz

I wonder if the program you are using to make the .tsv files is slipping in extra quotes, and this is confusing qiime. Try editing out the quotes let me know how that works.

Colin

6

I had tried without the quotes in a previous version, but it worked this time. I will flesh this out with more samples and give it a run through. The set of 5 worked.

7

There is a warning about underscores somewhere, but that has not been a problem for me yet.

8

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.