Error message associated with the metadata file

haadas · July 9, 2018, 4:48pm

Hello,
I am new to Qiime2. I have question regarding moving pictures tutorial. I have two fastq files coming from MiSeq and metadata file. I followed the tutorial with my files up to this command: qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree.qza --i-table table.qza --p-sampling-depth 1000 --m-metadata-file metadata2.txt --output-dir core-metrics-results
I get an error message like this when I run the command:
Plugin error from diversity:
None of the sample identifiers match between the metadata and the coordinates. Verify that you are using metadata and coordinates corresponding to the same dataset.
I enclose a PrtScn of the fastq file and the metadata (At the moment, I’ve just put in two examples)

I’d be happy to get help to understand where I’m wrong

Thanks,
Hadas

fastq file:

@M03023:134:000000000-B3KVP:1:1101:10774:2017 2:N:0:TCGCTGAACA
CCGTCATCCCCACCTTCCTCTCGGCTTATCACCGTCAGTCCCCTTATAGTTCCCAACTCAATTCTGGCAACTAAGGTCGATTGTTGCGCTCGTTGCGGTACTTAACCCAACATCTCACTACACGATCTGCCGACTGCCATTCATCACCTTTCTCCCCGTCCCGCAGCAACGCAACCGTCTCCGCTCACCTTCCTGTCATGTCCAGATCTTGTTAGGTTCTTCTCCTTTCTTTCACTTCAACCACATCCTCCTCCGCTTGTTCTCGCCCCCCTCCCTTTCTTTCACTTTTCCTCTTTCTCCC
+
-A,BC7FE@<C,@:EEE@FADF,,8CCFEA9CE:,8,,<EFEFFF,,,,<,<;6,,BC,,,<,<@,,;,,:6,,,,,:++,,,::,,+@4B+7?,,++,+8CA,,94>,,6+954A,>:,:,9+++94,,5++4++66,=,@,,6,466*6,3,@,++60*0+*+)+))***+)0::990*3)*1=*.:*74)*/*319*21,*)**(1**1***(0/***/*/)7.)7.;)))).1.)).((/,../)./(,/((,(,().6)((((-,(-(((,-)6)).))).))))).6<-462))(

metadata file:

#SampleID	BarcodeSequence	LinkerPrimerSequence	Description	InputFileName
Roni1.In.0	TCGAATGTGC	AACMGGATTAGATACCCKG	Roni1_In_0	
Roni2.Org.0	TCGCTGAACA	AACMGGATTAGATACCCKG	Roni2_Org_0

ebolyen · July 9, 2018, 5:02pm

Hey @haadas,

It sounds like your table.qza doesn’t have the same sample IDs as your metadata.

What does qiime feature-table summarize (without passing metadata as an argument) show for the sample IDs on that table?

haadas · July 25, 2018, 12:12pm

Hi,
There really were differences between the table and the metadata files.
Thanks for the help.
Hadas

bollergene · August 8, 2018, 5:53am

Dear Evan

I have similar issue on my data as reported here in the link

But my question is how will I know the the actual sample with the new sample ID as generated in the new table?

Thank you in anticipation
Bolaji

thermokarst · August 8, 2018, 11:41pm

Did you see this suggestion above?

bollergene · August 9, 2018, 6:00am

Thank you

Sorry for bothering you too much, I really appreciate for effort.
I saw the suggestion but my concern is the sampleID. I observed that my metadata sample ID is different from the one generated (sample 1 to 15). I don’t know which of my sample belong the ID sample1 to 15.
Please how do I know the sample that belong to each number (sample 1 to 15) so that I can change it accordingly in my metadata.

I run the below command to generate my table:
qiime feature-table summarize --i-table table.qza --o-visualization table.qzv

Thank you in anticipation.
Bolaji

thermokarst · August 9, 2018, 11:31pm

Hey there @bollergene!

No need to apologize, that is what we are here for!

QIIME 2 doesn't "generate" sample IDs - it uses the IDs that you provide, either via your metadata when demuxing, or as part of the import process. If there is a mismatch between IDs, you should take a look at your workflow and double-check what you did, since, as I mentioned, QIIME 2 doesn't make new Sample IDs for you.

If you want to attach your table.qzv and your sample metadata one of us can take a look.

How about following up with this info:

What version of QIIME 2 are you using?
What commands have you run to import your data? If you used a manifest file, please provide that here. If you used another format, please provide a few of your filenames here.

bollergene · August 10, 2018, 6:29am

Thank you,

I observed that I did not used metadata to import rather I used manifest as shown in the under listed commands. Thus I have attached my mainfest, metadata and table.qzv.
I am using qiime2-2018.6bolfatoyeyemi-manifest.txt (2.8 KB)
bolfatoyeyemi-metadata.tsv (1.1 KB)
table.qzv (412.1 KB)

qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path /Users/Bollergene/Documents/Metagenomics_15072018/bolfatoyeyemi-manifest --output-path /Users/bollergene/qiime2-bolaji/paired-end-demux.qza --source-format PairedEndFastqManifestPhred33.

Warm regards
Bolaji

thermokarst · August 10, 2018, 5:12pm

Thanks for sharing that information, @bollergene!

You defined that in your fastq manifest (bolfatoyeyemi-manifest.txt):

This file is one that you created in order to define which file (second column) belong to which sample (first column). Maybe it would make more sense for you to change the first column to match your sample IDs - whatever you put in that first column is the sample ID qiime 2 will use. Keep us posted!

bollergene · August 10, 2018, 6:07pm

Thank you for looking at it critically, Everything is clear to me now.
I have corrected it accordingly in my metadata and the under listed commands worked for me.
qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree.qza --i-table table.qza --p-sampling-depth 9428 --m-metadata-file /Users/bollergene/Documents/Metagenomics_15072018/bolfatoyeyemi-metadata.tsv --output-dir core-metrics-results

Warm regards
Bolaji

system · September 11, 2018, 12:07am

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