summary.tax error in v1.39

mothur bugs
1

Dear,

The summary.tax command isn’t working as expected in v1.39.
The summary file lacks taxlevel 1. Phyla information is in taxlevel 3, and there is no genera information.
If I run the same command with the same files in v1.38, everything works well.

Here are pieces of the outputs:

v1.39
"mothur > summary.tax(taxonomy=ok.taxonomy, count=ok.count_table)

It took 1 secs to create the summary file for 0 sequences.


Output File Names: ok.tax.summary"

------------------ ok.tax.summary in v1.39
taxlevel rankID taxon daughterlevels total R1 R2 R3 R4 S1 S2 S3 S4
0 0 Root 1 5824 728 728 728 728 728 728 728 728
2 0.1 Bacteria 14 5824 728 728 728 728 728 728 728 728
3 0.1.1 Acidobacteria 8 514 10 19 10 6 63 149 120 137
4 0.1.1.1 Acidobacteria_Gp1 8 265 6 18 7 3 30 50 69 82
5 0.1.1.1.1 Acidipila 1 3 0 0 0 0 1 0 2 0
6 0.1.1.1.1.1 Acidipila_unclassified 1 3 0 0 0 0 1 0 2 0
5 0.1.1.1.2 Acidobacteria_Gp1_unclassified 1 24 2 6 1 2 0 1 5 7

Version 1.38:

"mothur > summary.tax(taxonomy=ok.taxonomy, count=ok.count_table)

It took 0 secs to create the summary file for 2399 sequences.


Output File Names: ok.tax.summary " ----------------------ok.tax.summary in v1.38 taxlevel rankID taxon daughterlevels total R1 R2 R3 R4 S1 S2 S3 S4 0 0 Root 1 5824 728 728 728 728 728 728 728 728 1 0.1 Bacteria 14 5824 728 728 728 728 728 728 728 728 2 0.1.1 Acidobacteria 8 514 10 19 10 6 63 149 120 137 3 0.1.1.1 Acidobacteria_Gp1 8 265 6 18 7 3 30 50 69 82 4 0.1.1.1.1 Acidipila 1 3 0 0 0 0 1 0 2 0 5 0.1.1.1.1.1 Acidipila_unclassified 1 3 0 0 0 0 1 0 2 0 6 0.1.1.1.1.1.1 Acidipila_unclassified 0 3 0 0 0 0 1 0 2 0 4 0.1.1.1.2 Acidobacteria_Gp1_unclassified 1 24 2 6 1 2 0 1 5 7 5 0.1.1.1.2.1 Acidobacteria_Gp1_unclassified 1 24 2 6 1 2 0 1 5 7 6 0.1.1.1.2.1.1 Acidobacteria_Gp1_unclassified 0 24 2 6 1 2 0 1 5 7
Best regards
2

Could you try version 1.39.1, https://github.com/mothur/mothur/releases/tag/v1.39.1?

3

I tried and it worked fine. The tax.summary file now contains all taxa, including genera.
However, it is having some trouble to count the sequences involved in the process.
The output message from the command is still indicating 0 sequences
"
mothur > summary.tax(taxonomy=ok.taxonomy, count=ok.count_table)

It took 0 secs to create the summary file for 0 sequences.


Output File Names: ok.tax.summary" ---------------------------ok.tax.summary in v1.39.1 taxlevel rankID taxon daughterlevels total R1 R2 R3 R4 S1 S2 S3 S4 0 0 Root 1 5824 728 728 728 728 728 728 728 728 1 0.1 Bacteria 14 5824 728 728 728 728 728 728 728 728 2 0.1.1 Acidobacteria 8 514 10 19 10 6 63 149 120 137 3 0.1.1.1 Acidobacteria_Gp1 8 265 6 18 7 3 30 50 69 82 4 0.1.1.1.1 Acidipila 1 3 0 0 0 0 1 0 2 0 5 0.1.1.1.1.1 Acidipila_unclassified 1 3 0 0 0 0 1 0 2 0 6 0.1.1.1.1.1.1 Acidipila_unclassified 0 3 0 0 0 0 1 0 2 0
4

Thanks for bringing that to my attention. Also, I uploaded version 1.39.3 which corrects a bug in classify.seqs. You can download it here: https://github.com/mothur/mothur/releases/tag/v1.39.3.