I’ve been trying to run Microbiome Analyst tax4fun analysis using multiple data sets, but have not been able to generate the file with KO terms. Our data were processed using QIIME2 and mapped to the Silva database. We have uploaded ASV files that are in the same type format at the example dataset “Mammalian Gut.” Interestingly, when I run that sample dataset, tax4fun works fine.
My student did mention that the Silva database was updated. Is it possible that your code for the tax4fun module in microbiome analyst doesn’t work with the updated version? What else could be wrong?
Also, here is the R code from the analysis. When we try tax4fun, we just don’t get any result.
mbSet<-Init.mbSetObj()
mbSet<-SetModuleType(mbSet, “mdp”)
mbSet<-ReadSampleTable(mbSet, “ADB metadata.txt”);
mbSet<-Read16SAbundData(mbSet, “ADB ASV counts.txt”,“text”,“SILVA”,“T”);
mbSet<-SanityCheckData(mbSet, “text”);
mbSet<-PlotLibSizeView(mbSet, “norm_libsizes_0”,“png”);
mbSet<-CreatePhyloseqObj(mbSet, “text”,“SILVA”,“T”)
mbSet<-ApplyAbundanceFilter(mbSet, “prevalence”, 4, 0.2);
mbSet<-ApplyVarianceFilter(mbSet, “iqr”, 0.1);
mbSet<-PerformNormalization(mbSet, “rarewi”, “colsum”, “none”);
mbSet<-Perform16FunAnot(mbSet, “SILVA”,“qi_silva”);
Hello, thanks for posing this question. The problem was mainly caused by the “_” in your taxonomy labels which might be generated from the QIIME2 annotation pipeline. We have updated our tool to solve this issue. You can try again. Please let me know if you have more questions.
Best.
That did not seem to correct my problem. I changed all the underscores to spaces, but still get an error using tax4fun indicated a problem with the taxonomy labels. Did you successfully edit and then run my example file above?
Our website detected the redundant or error information more precisely currently. So would you please make the data in the right format and then test again?
I corrected the metadata file. Now there are no extraneous samples. But, I keep getting this error: “Error. Please check taxonomy labels”
I tried three iterations
1 - all underscores in taxonomy names replaced by a space, but left everything else alone
2 - all underscores in taxonomy names replaced by a space, and deleted [ and ] brackets
3 - left taxonomy labels as is, since your earlier post indicated you’d fixed your system to handle that.
4 - I also added back in the classification prefixes (k__;p__) to match exactly the format that is indicated in your help bubble for the file information on the opening screen.
I’m at a complete loss at this point.
Here are the corrected files. Can you please look again and tell me what else I need to do to fix this problem? If you’re successful (somehow), can you send me the output from tax4fun so we can just move forward?
Thanks for trying out. Actually, silva taxonomy does not need classification prefixes for processing, as you can see in our second example data. I removed the prefixes and it works. You can try again with the attached version. ADB_ASVcounts_corrected (1).txt (1.5 MB)
I am facing the exact same problem and I tried to use all informations (I think) in this post, but still Tax4fun is not working. “Error message: Please check taxonomy labels.”
The ASV_count file is attached: ASV_counts.txt (47.8 KB)
Can you find the mistake in my taxonomy labels?
Thanks in advance
Hello,
Could you please provide all the related files following our post guideline for trouble shooting ? I cannot process locally using the single file.
Thanks
sorry. My data was processed using Qiime2 and mapped with the SILVA database. Then I used the Marker Data Profiling. Everything works fine till I try tax4fun.
Sorry and this is my metadata file and the ASV_counts again which I used. metadata.txt (2.4 KB) ASV_counts.txt (47.5 KB)
I just started to change several things in my data till something was working. I managed that tax4fun is working when I sort only the first column (column A/ the taxonomy column) in Libre Office (.csv file). But now my data is completely wrong. If I undo this and the data would be correct it is not working anymore. Error is again: Check taxonomy labels. Files are attached. I am now completely confused. ASV_counts_unsorted_correct.csv (47.5 KB) ASV_counts_sorted_incorrect.csv (47.5 KB) metadata.txt (2.4 KB)
This is because in several samples, the abundance of the taxa that can be matched to the Tax4Fun inner-built library are all 0. We have updated the function. You can try again. But please read carefully of the warning messages which indicate the samples being removed during the processing.
