-s 'neisseria gonorrhoeae' return KeyError: '23S_rRNA_a2'

[Former user]

hi sir: -s 'neisseria gonorrhoeae'

 return  KeyError: '23S_rRNA_a2'

""" Traceback (most recent call last): File "~/resfinder/run_resfinder.py", line 501, in <module> id=sample_name) File "~/resfinder/cge/pointfinder.py", line 135, in old_results_to_standard_output db_name, gene_name, db['mis_matches'], True, db) File "~/resfinder/cge/pointfinder.py", line 1524, in get_mutations gene, look_up_pos, look_up_mut, m_type, gene_name) File "~/resfinder/cge/pointfinder.py", line 1742, in look_up_known_muts if pos in self.known_mutations[gene][mut]: KeyError: '23S_rRNA_a2' """

[CGE Helpdesk]

Dear Mr/Ms,

Thank you for the interest in ResFinder.

Could you kindly pass me the full command line that you have used?

And if possible, could you upload the data here: https://cge.cbs.dtu.dk/services/ResFinder/ and then pass the link to the results to this email: [e-mail]

Then we can more easily recreate your issue.

Kind regards,

Malene, CGE Helpdesk

[Hong Fei]

hi sir:

my detail command line as below:

“““

python ~/resfinder/run_resfinder.py -ifq GI_485_4757.non_nt.fastq.gz -o ./Resfinder -s 'neisseria gonorrhoeae' -db_res ~/resfinder_db
-acq -db_point ~/pointfinder_db --point -u -db_disinf ~/db_disinfinder -disinf
”””

get error same !!

thanks

[Kaixin h]

Hi ! Also came across a similar error, only for  'neisseria gonorrhoeae'; For other 4 species I tried, it works well.

Error: BLAST did not run as expected. The expected output file, /home/Results/Neisseria_gonorrhoeae/485.281/pointfinder_blast/tmp/out_23S_rRNA.xml, did not exist.
BLAST finished with the following response:

Command line argument error: Argument "subject". File is not accessible: `/home/user/resfinder/db_pointfinder/neisseria_gonorrhoeae/23S_rRNA.fsa'

‌

Hi Malene,

Could you pls have a try on this genomic data?

ftp://ftp.patricbrc.org/genomes/485.281

‌

Thanks!

[CGE Helpdesk]

Dear Hong Fei and Kaixin,

There has been a couple bug fixes in the program within the last few days, also in the neisseria_gonorrhoeae database. Could you please try to re-install the program (especially the pointfinder_db), and then please let me know if you still experience issues when running the program with the species neisseria gonorrhoeae specified.

Sorry for the inconvenience,

Kind regards,

Malene

[Kaixin h]

Seems no error now, thanks!

[Hong Fei]

hi sir:

‌ got another error after re-install and updata soft and database:

“““
Traceback (most recent call last):
File "~/Resfinder/20210418/resfinder/run_resfinder.py", line 486, in <module>
id=sample_name)
File "~/Resfinder/20210418/resfinder/cge/pointfinder.py", line 135, in old_results_to_standard_output
db_name, gene_name, db['mis_matches'], True, db)
File "~/Resfinder/20210418/resfinder/cge/pointfinder.py", line 1524, in get_mutations
gene, look_up_pos, look_up_mut, m_type, gene_name)
File "~/Resfinder/20210418/resfinder/cge/pointfinder.py", line 1742, in look_up_known_muts
if pos in self.known_mutations[gene][mut]:
KeyError: 'macAB_promoter_size_225'

“““

[CGE Helpdesk]

Dear Hong Fei,

I would like to take a closer look on why your job fails.

If possible, could you upload the data here: https://cge.cbs.dtu.dk/services/ResFinder/ and then pass the link to the results to this email: [e-mail] (and write in the email that it is regarding Resfinder issue #43).

Then we can more easily recreate the issue.

Kind regards,

Malene

[Kaixin h]

if pos in self.known_mutations[gene][mut]:
KeyError: 'macAB_promoter_size_225'

Hi, I also come across this same error. I am wondering if this error is solved or not?

BTW, I can’t upload the data via the website, because I change the codes in run_resfinder.py a little to make Resfinder able to run fna files with KMA instead of Blastn.

With Blastn , there is no error. And I think this error is not caused by my change(and my change works for other species), as this error happens at pointfinder.py.

‌

Best,

Kaixin

‌

[Alfred Ferrer Florensa]

Hi Kaixin,

We could not solve the error because we are not able to reproduce it, and we did not receive any email from the user. However, if you have found the same error, could you upload the data that gives you that error to the webserver  https://cge.cbs.dtu.dk/services/ResFinder/ and then pass the link to the results to this email: [e-mail] (and write in the email that it is regarding Resfinder issue #43).

‌

About the uploading the data to the website (https://cge.cbs.dtu.dk/services/ResFinder/), there is no relationship between the code run_resfinder.py and the webserver. However, if the problem is in your local version, I would not change KMA for Blastn when using fasta files.

‌

Best,

Alfred

[Kaixin h]

Hi Alfred, thanks for your reply. The web runs well.

I guess in my local version, it seems that the output result of kma_run was changed from macAB_promoter_size_225bp to macAB_promoter_size_225.

Anyway, I can use Blastn. That’s fine.

[Alfred Ferrer Florensa]

Hi Kaixin,

The web runs with the last versions of KMA/software/databases. If you have a problem but it does not appear in the webpage, maybe is related to your local versions.

Our software has been designed so KMA is used on raw reads and blastn on assembled data.

[Kaixin h]

Hi  Alfred, the data I fed in is assembled data, so I guess the web runs it with  blastn, not kma.

My local version based on blastn also runs well.

[Alfred Ferrer Florensa]

Then I will close this thread.