TypeError: can only concatenate str (not "NoneType") to str

[dustin-dial]

Hello,

First, I wanted to thank you for creating such a great tool, it has already proven to be very useful! However, when I run the annotate command, I get an error after the blastp/blastx search and extraction stages when the program is trying to write the summary file. Here's the command I used on the Tremblaya .gbf file for a test run with the sprot db:

python3 /home/dtdial/pseudo-finder/pseudofinder.py annotate --genome /home/dtdial/pseudo-finder/test/candidatus_tremblaya_princeps_PCIT.gbf --outprefix test --database /home/dtdial/Bacteria/sprot --threads 16

And this is the error message:

2020-08-16 18:11:50     CDS extracted from:                     /home/dtdial/pseudo-finder/test/candidatus_tremblaya_princeps_PCIT.gbf
                        Written to file:                        test_cds.fasta.
2020-08-16 18:11:50     Proteome extracted from:                /home/dtdial/pseudo-finder/test/candidatus_tremblaya_princeps_PCIT.gbf
                        Written to file:                        test_proteome.faa.
2020-08-16 18:11:50     Intergenic regions extracted from:      /home/dtdial/pseudo-finder/test/candidatus_tremblaya_princeps_PCIT.gbf
                        Written to file:                        test_intergenic.fasta.
2020-08-16 18:11:50     blastp executed with 16 threads.
2020-08-16 18:11:51     blastx executed with 16 threads.
2020-08-16 18:11:53     Extracting information from blastp file.
2020-08-16 18:11:53     Extracting information from blastx file.
2020-08-16 18:11:53     Checking contig 1 / 1 for pseudogenes.
                        Number of ORFs on this contig: 186
                        Number of pseudogenes flagged: 18
2020-08-16 18:11:53     Writing summary of run: test_log.txt
Traceback (most recent call last):
  File "/home/dtdial/pseudo-finder/pseudofinder.py", line 30, in <module>
    annotate.main()
  File "/home/dtdial/pseudo-finder/modules/annotate.py", line 1339, in main
    write_summary_file(args=args, file_dict=file_dict)
  File "/home/dtdial/pseudo-finder/modules/annotate.py", line 948, in write_summary_file
    "Functional genes:\t" + str(StatisticsDict['ProteomeOrfs'] - StatisticsDict['FragmentedOrfs'] - StatisticsDict['PseudogenesShort'] - StatisticsDict["dnds"]) + "\n\n"
TypeError: can only concatenate str (not "NoneType") to str

I have the same issue when I run the command on other .gbk/.gbf files generated by prokka with the recommended settings and when I use the NR database. I do get all of the expected outputs, but the log file is empty, and I'd like to use the reannotate command.

Thank you!

[mitchso]

Hi Dustin,

Sorry for the delay, I've been overhauling some of the inner workings and this bug should be solved. Can you pull the updates and try again?

Cheers, Mitch

[dustin-dial]

Mitch,

It works like a charm! Thanks again!

Best,

Dustin

[mitchso]

Glad to hear it! No problem, closing this issue