Why I can't do alpha and beta diversity?

[CHIA]

Hi all, I am currently having a raw shotgun metagenome sequencing data. I am currently using the QIIME moshpit to run my data. So far, I have done

1. Create a manifest file in tsv

2. Change tsv file to qza (output: RD1_RD14_paired-end-demux.qza)

3. Classify sequences against Kraken2 database (output: RD1_RD14_kraken2-classification.qza and RD1_RD14_kraken2_output.qza)

4. Visualize the kraken2 classification results (input: RD1_RD14_kraken2-classification.qza ; output RD1_RD14_species_taxonomy.qza)
   

   

5. Visualize species taxonomy (input: RD1_RD14_species_taxonomy.qza ; output: RD1_RD14_species_taxonomy.qzv)
   

   

However, when I try to do the alpha diversity, I am unable to proceed

qiime diversity alpha \
> --i-table RD1_RD14_species_table.qza \
> --p-metric shannon \
> --o-alpha-diversity RD1_RD14_shannon_vector.qza
Plugin error from diversity:

  Parameter 'table' requires an argument of type FeatureTable[Frequency | RelativeFrequency]. An argument of type FeatureTable[PresenceAbsence] was passed.

Debug info has been saved to /tmp/qiime2-q2cli-err-3z6dzd49.log

I have try to search for solution yet I still unable to resolve this problem.

Looking forwards from someone who can help me resolve this, thank you in advance!

[SoilRotifer (Mike Robeson)]

Hi @CHIA,

This message:

Parameter 'table' requires an argument of type FeatureTable[Frequency | RelativeFrequency]. An argument of type FeatureTable[PresenceAbsence] was passed.

tells us, that your RD1_RD14_species_table.qza is of FeatureTable[PresenceAbsence] table and it should be either a FeatureTable[Frequency or a RelativeFrequency] table. That is, the table you supplied to the command only annotates if a feature is present or absent, where as you ned to supply a tbale with actual counts. What command did you use to import / generate this file?