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
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Create a manifest file in tsv
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Change tsv file to qza (output: RD1_RD14_paired-end-demux.qza)
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Classify sequences against Kraken2 database (output: RD1_RD14_kraken2-classification.qza and RD1_RD14_kraken2_output.qza)
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Visualize the kraken2 classification results (input: RD1_RD14_kraken2-classification.qza ; output RD1_RD14_species_taxonomy.qza)
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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!