FROGSSTAT Phyloseq Import Data.

[reemelkabbout]

Hey guys. I hope you're doing fine. I'm trying to create the phyloseq object in FROGS for further analysis. Every time I get the same error : "Your biom input file is not comming from FROGS and has no standard taxonomy metadata". I don't why. I tried it before on other data and it worked well. Input file BIOM is: "FROGS BIOM to std BIOM: abundance.biom". Error : Traceback (most recent call last): File "/projet/gxyprod/galaxy/database/dependencies/_conda/envs/__frogs@3.1.0/bin/r_import_data.py", line 143, in raise Exception("Your biom input file is not comming from FROGS and has no standard taxonomy metadata.\n") Exception: Your biom input file is not comming from FROGS and has no standard taxonomy metadata.

Anyone can help me, please ?

[mariabernard]

Hi,

The code that generates this error, looks for "taxonomy" tag (standard taxonomy metadata tag) or "blast_taxonomy" tag (FROGS taxonomy tag obtained by Blast+) in your biom file. Are you shure that you used the biom file after the FROGS Affiliation step ?

[reemelkabbout]

Hi Maria, Here are the steps that I've done: 1) Pre-processing 2) Clustering + Cluster Stat 3) Remove chimera 4) Filtration 5) Affiliation + Affiliation Stat 6) Phylogenetic Tree And now I'm trying to create the phyloseq object. The affiliation step generates a Biom file that I used for phylogenetic tree construction. And then I converted the Biom file of affiliation to standard Biom. I used that Biom standard file to create the phyloseq object + tree + metadata, but it didn't work.

[reemelkabbout]

This is how the affiliation BIOM file looks like. I think it does contain the taxonomy tags obtained by Blast, right?

[mariabernard]

right!

Could you filter this biom file, to keep, let's say, the 3 most abundant OTU with FROGS Filter. Try to import this reduced biom file into phyloseq. If the error is still present, do you accept to send me this reduced file ? ... email hidden ... If there is no error, could you send me the entire file ?

[mariabernard]

As we discuss by email, you solved this error but you have an other error with unprecised message.

I do not wrap R Error message. This is on my todo list.

The most frequent error for this tool is inconsistency between sample list name in your metadat TSV file and in the abundance.biom file. To check this, you can :

• convert your biom file in TSV file thanks to FROGS biom_to_tsv tools. This will be easier to read the abundance file and check the sample name.

• or look into any html report from previous step, there are multiple table that describe sample so you can extract sample names from these table.

  In your biom file that you sent me, the sample names are : Orge37ITS and Orge42ITS

In your sample metadata file its : 19LIB015-19MET228_S226_L001 and 19LIB015-19MET231_S229_L001

Simply use the same names in your sample metadat file and it works.

You asked me an other question about how to filter abundance on the presence in this 2 samples. Use the FROGS Filters tools, with "Apply Filter" in the "*** THE FILTERS ON OTUS IN SAMPLES, OTUS SIZE and SEQUENCE PERCENTAGE" section, and write 2 in "Minimum number of samples", you biom file contain only this 2 samples isn't it ? Do the filter step before importing abundance into FROGSSTAT Phyloseq import tools

Hope everything will work for you.

Regards