ERROR: This has possibly been a NUCmer run failure, please investigate > ERROR: NoneType: None about pyani

[baileythegreen]

@neelam, the second set of errors you added here look to be the same kind of error you were originally asking about, so the answers provided by @widdowquinn will also apply.

Please investigate the first two possibilities mentioned by @widdowquinn, to see if they resolve the issue.

Note: with the first option, he was not suggesting using an entirely different dataset, per se, but that you try removing only those genomes which resulted in the failed comparison, to see if the run then completed without error.

We'll look for your response, but if no further information as to the ultimate cause of the errors is added, or other update provided, within the next month, this issue will be closed. (You can always still respond to it, and it can be re-opened, if needed.)

[widdowquinn]

Hi @neelam19051

Thank you for using pyani!

The error message is asking you to check the outputs of two of your comparisons involving the E90 isolate - one against P9W and one against AR 458. pyani is finding that the algnment runs suggest there are no regions of similar sequence between the two genomes, in each case.

There is more than one possible reason for this.

• it may be the case that there are no similar regions in those genomes; if this is the case you may wish to change your set of input genomes to remove an uninformative comparison
• it may be that the nucmer comparison has failed for a technical reason; to check this, please try running the corresponding nucmer command (if you are using the -l logging, and/or the -v verbose output you should be able to see the set of commands that are run, and that may help you)
• it may be that there is a bug or other issue in the pyani code; there is not enough information to determine this, at the moment and you should first investigate the two options above, to eliminate those possibilities

I hope this is useful - please do ask further questions and report your results in this issue thread.

L.

[neelam19051]

Hi, when i use pyani on a different datasets, it gives following error-

INFO: Cumulative return value: 10
WARNING: At least one NUCmer comparison failed. ANIm may fail.
INFO: Processing NUCmer .delta files.
WARNING: Total alignment length reported in clust4.2/AMR_ANIm_output/nucmer_output/P_aeruginosa_Pa124_vs_P_aeruginosa_AR_0357.filter is zero!
WARNING: Total alignment length reported in clust4.2/AMR_ANIm_output/nucmer_output/P_aeruginosa_Pa124_vs_P_aeruginosa_AR_0095.filter is zero!
WARNING: Total alignment length reported in clust4.2/AMR_ANIm_output/nucmer_output/P_aeruginosa_Pa124_vs_P_aeruginosa_SP4527.filter is zero!
WARNING: Total alignment length reported in clust4.2/AMR_ANIm_output/nucmer_output/P_aeruginosa_Pa124_vs_P_aeruginosa_FDAARGOS_571.filter is zero!
WARNING: Total alignment length reported in clust4.2/AMR_ANIm_output/nucmer_output/P_aeruginosa_Pa124_vs_P_aeruginosa_SP4371.filter is zero!
WARNING: Total alignment length reported in clust4.2/AMR_ANIm_output/nucmer_output/P_aeruginosa_Pa124_vs_P_aeruginosa_PSE6684.filter is zero!
WARNING: Total alignment length reported in clust4.2/AMR_ANIm_output/nucmer_output/P_aeruginosa_Pa124_vs_P_aeruginosa_LYSZa7.filter is zero!
WARNING: Total alignment length reported in clust4.2/AMR_ANIm_output/nucmer_output/P_aeruginosa_Pa124_vs_P_aeruginosa_SP4528.filter is zero!
WARNING: Total alignment length reported in clust4.2/AMR_ANIm_output/nucmer_output/P_aeruginosa_Pa124_vs_P_aeruginosa_AR_0353.filter is zero!
WARNING: Total alignment length reported in clust4.2/AMR_ANIm_output/nucmer_output/P_aeruginosa_Pa124_vs_P_aeruginosa_FDAARGOS_501.filter is zero!
WARNING: Total alignment length reported in clust4.2/AMR_ANIm_output/nucmer_output/P_aeruginosa_Pa124_vs_P_aeruginosa_C79.filter is zero!
ERROR: This has possibly been a NUCmer run failure, please investigate
ERROR: NoneType: None

Thank you

[widdowquinn]

Hi, can you please tell me how to give lable.txt and class.txt file for those genome which are not downloaded by pyani download option ..i mean i want to label ani result but i don't have this two files because i had already downloaded data.

As this is a different question to the original I've moved it to a new issue: #394