%i format: a number is required, not NoneType

[eam12]

I am trying to use the very large external scheme Enterobase Salmonella cgMLSTv2. After running chewBBACA.py PrepExternalSchema, I tried running chewBBACA.py AlleleCall, but I get the following errors. First, 'utf-8' codec can't decode byte is repeated over and over again and then I get the following repeated over and over again:

some error occurred
%i format: a number is required, not NoneType
Error on line 466

I did get output files, but there are many ERRORs in the results_alleles.tsv file. As far as I can tell, PrepExternalSchema ran correctly, minus the removal of two loci with no correct alleles (I'm assuming they're not complete CDS). If the input scheme is correct, do the errors I'm getting have to do with the contig FASTA files I'm using? Any help would be much appreciated. Thank you!

[rfm-targa]

Greetings,
Can you please check what's the Python version that is being called when running chewBBACA? It should be executed with Python>=3.4 just to be safe.

[eam12]

I double checked and I'm running chewBBACA with python 3.6.7 (as is the default in bioconda).

[eam12]

Just an update, I realized there may have been an incompatibility issue between the version of python installed from bioconda (3.6.7) and the version I had running in the computer cluster I'm using (3.6.3). However, after uninstalling the cluster version of python I had running, but I am still getting the same error messages when I run chewBBACA.py AlleleCall:

Checking all prodigal processes created the necessary files...
All prodigal files necessary were created

Finishing Prodigal at : 11:20:02-29/07/2019
Translating genomes
Starting Genome Blast Db creation at : 11:21:21-29/07/2019
Starting Allele Calling at : 11:21:40-29/07/2019
Processing STM4351.fasta. Start 11:21:40-29/07/2019 Locus 13 of 3000. Done 0%.some error occurred
%i format: a number is required, not NoneType
Error on line 466
some error occurred
%i format: a number is required, not NoneType
Error on line 466
some error occurred
%i format: a number is required, not NoneType

etc.

[rfm-targa]

Can you please confirm if you get the same errors with the tutorial? It is possible that something in the new schema is leading to that problem and running the tutorial would help us figure that out.

[eam12]

I can run chewBBACA.py CreateSchema -i complete_genomes/ --cpu 6 -o schema_seed --ptf Streptococcus_agalactiae.trn successfully, but when I run chewBBACA.py AlleleCall -i complete_genomes/ -g schema_seed/ -o results_cg --cpu 6 --ptf Streptococcus_agalactiae.trn I get the same errors as I get with my new schema:

Finishing Prodigal at : 12:42:02-29/07/2019
Translating genomes
Starting Genome Blast Db creation at : 12:42:14-29/07/2019
Starting Allele Calling at : 12:42:17-29/07/2019
Processing GCA-000007265-protein51.fasta. Start 12:42:17-29/07/2019 Locus 5 of 3130. Done 0%.some error occurred
%i format: a number is required, not NoneType
Error on line 466
some error occurred
%i format: a number is required, not NoneType
Error on line 466
some error occurred
%i format: a number is required, not NoneType
Error on line 466
some error occurred

etc.

[mickaelsilva]

prodigal version and chewbbaca version?

[eam12]

prodigal v.2.6.3
chewbbaca v.2.0.16

[rfm-targa]

We suggest that you install the latest version of chewBBACA and necessary dependencies. Use the version that is in this repository and not the version available in Conda. Retry the tutorial and please tell us if you still encounter the same problem. Not being able to successfully run the tutorial indicates that it might be a problem or conflict with software (and not because there is an issue with the data), so please update to the latest stable version.

[eam12]

I installed the latest version of chewBBACA (2.0.17) and its dependencies using pip3 install chewbbaca --user. Dependency versions:

• numpy 1.17.0
• scipy 1.3.0
• biopython 1.74
• plotly 4.0.0
• SPARQLWrapper 1.8.4
• pandas 0.25.0
• BLAST+ 2.8.1
• Prodigal 2.6.3

I am still getting the same error messages when I run chewBBACA.py AlleleCall -i complete_genomes/ -g schema_seed/ -o results_cg --cpu 6 --ptf Streptococcus_agalactiae.trn.

[rfm-targa]

What is the system that you're using to run chewBBACA? If you haven't tried to run on a different system, please try to do so and let us know if you get the same error even after switching to another system. With all dependencies and the correct versions, the tutorial should complete successfully. Your problem might be related with the configuration of your current environment or other system-related issue.

[vvunderkin]

Hi I'm just going to piggy back on this.

I posted in the thread on the tutorial repo about this same issue. I've updated all of my dependencies. Used the chewBBACA that is available on both conda and pip3, and have tried it on both my work UBUNTU station and my personal MacBook Air. They all come up with the same 466 error. But for some reason the first part of the tutorial also works entirely, i.e. I can produce the image from the first section of the tutorial--the one with the 95% plot.

I don't know what to do. Any further analyses I try to do won't work however :(

[mickaelsilva]

@eam12 @jeremiahyarmie the issue should be now fixes. Latest updates from biopython were giving error when trying to print(match) for some reason

should be working now on 2.0.17.2

let me know if it worked

[vvunderkin]

it's working thank you!!!!! :')