# Strainphlan\_config & line 655 TypeError

**URL:** <https://forum.biobakery.org/t/strainphlan-config-line-655-typeerror/534>\
**Category:** PhyloPhlAn\
**Created:** [May 30, 2020, 2:14pm UTC](https://forum.biobakery.org/t/strainphlan-config-line-655-typeerror/534 "2020-05-30T14:14:37Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![michaelwoodworth](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/michaelwoodworth/32/496_2.png) [@michaelwoodworth](https://forum.biobakery.org/u/michaelwoodworth)\
**Post date:** [May 30, 2020, 2:14pm UTC](https://forum.biobakery.org/t/strainphlan-config-line-655-typeerror/534/1 "2020-05-30T14:14:37Z")

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Hello,

Thanks for developing and supporting these great tools. I’m working with the StrainPhlan 3.0 wiki, in a conda-installed environment with metaphlan 3.0 (20 Mar 2020) & phylophlan 3.0.51 (11 May 2020).

I’m on step 5 of the wiki ([https://github.com/biobakery/MetaPhlAn/wiki/StrainPhlAn-3.0](https://github.com/biobakery/MetaPhlAn/wiki/StrainPhlAn-3.0)). I’m getting multiple errors with this step as below:

strainphlan -s consensus\_markers/\*.pkl -m db\_markers/s\_\_  
Escherichia\_coli.fna -r genomes/E\_coli\_group\_FMT3.fna -o output -n 10 -c s\_\_Escherichia\_coli --mutation\_rat  
es  
Sat May 30 09:54:09 2020: Start StrainPhlAn 3.0 execution  
Sat May 30 09:54:09 2020: Creating temporary directory…  
Sat May 30 09:54:09 2020: Done.  
Sat May 30 09:54:09 2020: Getting markers from main sample files…  
Sat May 30 09:54:09 2020: Done.  
Sat May 30 09:54:09 2020: Getting markers from main reference files…Warning: [blastn] Examining 5 or more  
matches is recommended

Sat May 30 09:54:10 2020: Done.  
Sat May 30 09:54:10 2020: Removing bad markers / samples…  
Sat May 30 09:54:10 2020: Done.  
Sat May 30 09:54:10 2020: Writing samples as markers’ FASTA files…  
Sat May 30 09:54:10 2020: Done.  
Sat May 30 09:54:10 2020: Writing filtered clade markers as FASTA file…  
Sat May 30 09:54:10 2020: Done.  
Sat May 30 09:54:10 2020: Calculating polymorphic rates…  
Sat May 30 09:54:10 2020: Done.  
Sat May 30 09:54:10 2020: Executing PhyloPhlAn 3.0…  
Sat May 30 09:54:10 2020: Creating PhyloPhlAn 3.0 database…  
Sat May 30 09:54:10 2020: Done.  
Sat May 30 09:54:10 2020: Generating PhyloPhlAn 3.0 configuration file…  
Sat May 30 09:54:10 2020: Done.  
Sat May 30 09:54:10 2020: Processing samples…[e] “/home/mwoodwo/anaconda3/envs/metaphlan3/lib/pytho  
n3.7/site-packages/phylophlan/phylophlan\_configs/” folder does not exists

Sat May 30 09:54:13 2020: Done.  
Sat May 30 09:54:13 2020: Done.  
Sat May 30 09:54:13 2020: Writing information file…Traceback (most recent call last):  
File “/home/mwoodwo/anaconda3/envs/metaphlan3/bin/strainphlan”, line 10, in   
sys.exit(main())  
File “/home/mwoodwo/anaconda3/envs/metaphlan3/lib/python3.7/site-packages/metaphlan/strainphlan.py”, line  
830, in main  
args.mutation\_rates, args.print\_clades\_only, args.nprocs)  
File “/home/mwoodwo/anaconda3/envs/metaphlan3/lib/python3.7/site-packages/metaphlan/strainphlan.py”, line  
790, in strainphlan  
phylophlan\_mode, nprocs)  
File “/home/mwoodwo/anaconda3/envs/metaphlan3/lib/python3.7/site-packages/metaphlan/strainphlan.py”, line  
655, in write\_info  
"\nNumber of processes used: "+ str(nprocs)) + “\n”  
TypeError: unsupported operand type(s) for +: ‘int’ and ‘str’

- Is there a recommended step for creating a phylophlan\_config directory?
- Are there any workarounds for the TypeError you might suggest?

thanks!

Mike

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**Author:** ![f.asnicar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/f.asnicar/32/196_2.png) [@f.asnicar](https://forum.biobakery.org/u/f.asnicar)\
**Post date:** [June 1, 2020, 10:22am UTC](https://forum.biobakery.org/t/strainphlan-config-line-655-typeerror/534/2 "2020-06-01T10:22:03Z")

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Hello Mike, thanks for reporting this.  
I’m tagging @aitor.blancomiguez who is developing StrainPhlAn as I believe your error is on the StrainPhlAn side and not on PhyloPhlAn.

Thanks,  
Francesco

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**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [June 1, 2020, 10:31am UTC](https://forum.biobakery.org/t/strainphlan-config-line-655-typeerror/534/3 "2020-06-01T10:31:25Z")

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> [@michaelwoodworth](#):
>
> /home/mwoodwo/anaconda3/envs/metaphlan3/lib/pytho  
> n3.7/site-packages/phylophlan/phylophlan\_configs/

Hello Mike,  
The problem seem to be a missing folder. Could you please create the following directory:  
/home/mwoodwo/anaconda3/envs/metaphlan3/lib/pytho  
n3.7/site-packages/phylophlan/phylophlan\_configs/  
I think this will solve your problem

Best,  
Aitor