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

[Yuanzhou-W]

failed running with a different format fasta doc while running the following line:

average_nucleotide_identity.py -i  //genome -o  //pyani_result -m ANIm -g -v --write_excel -l log.txt -f

Current Output:

WARNING: At least one NUCmer comparison failed. ANIm may fail.
WARNING: Total alignment length reported in //uncultured_Prochlorococcus_sp._AG-895-I05_vs_HLII-1_XMU1423-d.filter is zero!
WARNING: Total alignment length reported in //uncultured_Prochlorococcus_sp._AG-453-M02_vs_HLII-1_XMU1426-d.filter is zero!
WARNING: Total alignment length reported in //Prochlorococcus_sp._AG-355-I04_vs_HLII-1_XMU1425-d.filter is zero!
ERROR: This has possibly been a NUCmer run failure, please investigate
ERROR: NoneType: None

pyani Version:

0.2.12

Operating System:

ubuntu 14.04

We have investigated the issue of the sequence file error. Ultimately, the possible cause of the error could be the inconsistent line length in the FASTA file: different number of characters per line led to the error. The files that triggered the error had eighty characters per line for some and sixty characters per line for others. The errors only occurred when comparing FASTA files of different formats. After standardizing the format (eighty characters per line for all or sixty characters per line for all), the error disappeared. No further testing was done.

[ZiliaMR]

How exactly did you solve the problem? I have this error and I have standardised the fasta files (80 characters for each line) and I still have the problem. I am using contigs level assemblies.

[widdowquinn]

Hi @ZiliaMR - if your NUCmer run is failing there are two likely possibilities:

1. One of the pairwise genome comparisons is between two organisms that are so dissimilar NUCmer cannot find any points of similarity
2. NUCmer has been unable to run for some other reason (this can happen if, for example, there is whitespace in a filename)

Your first action should be to examine the output (if any) for the comparison that pyani is indicating has a problem, and try to rerun the NUCmer comparison independently. This will usually indicate one of the two situations above. To resolve it, either remove one of the unrelated genomes from the analysis, or fix the NUCmer issue that is reported.

L.

[ZiliaMR]

Thanks so much! :) I found the error. I have another question but I will open an issue for it.