converting from Mothur to Qiime

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Jean-Francois Martin

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Jan 20, 2016, 9:10:19 AM1/20/16
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dear all,
I did my OTU picking with mothur and converted the OTU table to biom with the command

make.biom(shared=stability.trim.contigs.good.unique.good.filter.unique.precluster.abund.pick.pick.an.unique_list.shared, constaxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.abund.pick.pick.an.unique_list.0.03.cons.taxonomy)

the produced biom file works with a couple of Qiime (1.9.1) scripts as plot ones but I could not make it work with

core_diversity_analyses.py with an error : ValueError: Shape tuple is incompatible with data.


I could not find whether the problem comes from my biom or my mapping file.

I join the files that I think may be useful for anyone wanting to hep me. It may be something stupid but I could not find it after two days and did not find any related post on the forum yet.

I hope someone can help.


Thanks a lot,

Jef

stability.trim.contigs.good.unique.good.filter.unique.precluster.abund.pick.pick.an.unique_list.shared
mapping.txt
stability.trim.contigs.good.unique.good.filter.unique.precluster.abund.pick.pick.an.unique_list.0.03.biom

justink

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Jan 20, 2016, 10:51:06 PM1/20/16
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Odd. it appears to be specific to rewriting in hdf5 format. Looking into it.

Jai Ram Rideout

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Jan 21, 2016, 11:13:47 AM1/21/16
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Hi Jef,

Can you please provide the following info?

1. The output from running: print_qiime_config.py -t
2. The exact core_diversity_analyses.py command you're running

Jai

Husen Zhang

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Jan 23, 2016, 11:46:25 AM1/23/16
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I encountered the same problem and found a workaround: 

First convert the mothur-made biom to the classic tsv format, then back to json:

qiime
biom convert -i v1v3_subset_0.03.biom -o v1v3_subset_0.03.txt --to-tsv --header-key taxonomy
biom convert -i v1v3_subset_0.03.txt -o v1v3roundTrip.biom --to-json --process-obs-metadata taxonomy --table-type "OTU table"
summarize_taxa_through_plots.py -i v1v3roundTrip.biom -o test -m qiime_mapping_v1v3_subset.tsv -c Treatment

Husen

Jean-Francois Martin

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Jan 25, 2016, 4:14:28 AM1/25/16
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First of all thank you both for your help, I greatly appreciate that.

@ Jai Ram Rideout : I attach the result of the config command. I use the virtual machine as provided at the Qiime web site.
the core_diversity command I use is : core_diversity_analyses.py -i file.biom -o ./output -m mapping.txt -e 8413 --nonphylogenetic_diversity
As you will see on the next line, the probleme is kind of solved but I am still curious to know where it comes from if you can find it I thnink it will be helpful to many people.

@ Husen Zhang : thanks a lot ! your workaround worked perfectly for me ! you save my day !

Thanks again,
Jef
config_qiime.txt

Jai Ram Rideout

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Jan 25, 2016, 2:18:05 PM1/25/16
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Thanks for the workaround Husen, and thanks for the details Jef! There are a couple of other workarounds in this thread, as well as details about the problem itself and why the workarounds are necessary.

Hope this helps,
Jai

Jean-Francois Martin

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Jan 26, 2016, 2:21:13 AM1/26/16
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Thank you again. I am lucky that the Qiime community is very active!
Cheers
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