biom error: cannot convert null to a float

Commands in mothur
1

Hi,
I get a “cannot convert null to a float” error after runing the picrust option in make.biom, although I do get an output. I’m wondering if the error has to do with my cons file not having the empty taxonomies of “incomplete” classifications.
Many thanks.
Pedro.

2

Are you using version 1.33.1?

3

Hi Sara,
Yes, I’m using v. 1.33.1. Despite the error message, the biom file still works in picrust…
Thank you.

4

Could you send me the log file and input files? I would like to track down the issue. Thanks.

5

Hi,

I am trying to build an biom table to use with picrust using the commands I found in another post:
classify.seqs(fasta=andrei.unique.good.good.filter.unique.precluster.pick.fasta, name=andrei.unique.good.good.filter.unique.precluster.pick.names, group=andrei.good.good.pick.groups, template=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, cutoff=80, processors=8)
classify.seqs(fasta=current, taxonomy=gg_13_5_99.gg.tax, reference=gg_13_5_99.fasta) ##### reclassify to greengenes
classify.otu(taxonomy=current, name=final.names, list=final.an.list) ###### find consensus taxonomy
make.biom(shared=final.an.shared, label=0.03, reftaxonomy=gg_13_5_99.gg.tax, constaxonomy=final.an.0.03.cons.taxonomy, picrust=97_otu_map.txt)

I get the tables but I also get the “cannot convert null to a float” error.
I am using mothur version 1.33.3

Manuel

6

Could you send your input files to mothur.bugs@gmail.com?

7

I have just sent the files,

Manuel

8

I am having the same issue.
Did you solve the problem?
Thanks
Caio

9

Same issue here using mothur v.1.33.3. Make.biom does generate the .biom and .shared files but there seems to be an issue with the sub-sampling. I tried to open the generated .biom file in MEGAN, it appears that for some of the samples there was an issue with the number of reads (e.g. >140000000 for one sample which is crazy). This only happens when using the picrust option though. Has a solution been found for this problem?

Thanks

10

We have yet to get files from anyone, so if you can send us the files along with the exact command you are running that would be great. Also, if you could reference this thread’s url that would help.

Pat

11

Hi All,

Maybe the MOTHUR team already found a solution (update 1.34.0). Nevertheless, the possible cause of showing a “cannot convert null to a float” error after running the picrust option in make.biom is because some missing values in the taxonomy file generated after classify.otu.

For example:

Otu0020 8 Root(100);k__Bacteria(100);p__Proteobacteria(100);c__Alphaproteobacteria(100);o__Sphingomonadales(100);
f__Erythrobacteraceae(100);;


if you add the percentage value in the missing taxonomy (see below):

Otu0020 8 Root(100);k__Bacteria(100);p__Proteobacteria(100);c__Alphaproteobacteria(100);o__Sphingomonadales(100);
f__Erythrobacteraceae(100);;


The message did not appear. I generated biom files using both taxonomy files (unedited and edited files) and no difference was observed.
12

Thank you for reporting this, and helping us make mothur as bug free as possible. Classify.otu will be modified in 1.34.0 to include the confidences for unclassifieds.

13

Hello,

I am facing the similar problem (v.1.33.3) [ERROR]: cannot convert null to a float., is it OK to use the output files in picrust?

Many thanks,

14

Hi ozgul,

Following the suggestion from the previous email, I generated two output files (with and without the [ERROR]: cannot convert null to a float) using the same data.

I explored the biom.shared files from the two independent runs and both files look identical. I presume is OK to used the file in picrust.