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donovan-h-parks / CompareM

A toolbox for comparative genomics.
GNU General Public License v3.0
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TypeError: cannot unpack non-iterable NoneType object #31

Open dikshyantg opened 4 years ago

dikshyantg commented 4 years ago

Hi, I was trying to perform comparM aai_wf on two genomes of bacteria . I used the command aai_wf mygenomes out --proteins The error I received was -

[2020-05-16 10:35:23] INFO: CompareM v0.1.1 [2020-05-16 10:35:23] INFO: comparem aai_wf mygenomes out --proteins [2020-05-16 10:35:23] WARNING: Changing file extension from 'fna' to 'faa' since 'proteins' flag was given. [2020-05-16 10:35:23] INFO: Appending genome identifiers to query genes. [2020-05-16 10:35:23] INFO: Creating DIAMOND database (be patient!). [2020-05-16 10:35:23] INFO: Performing self similarity sequence between genomes (be patient!). [2020-05-16 10:35:30] INFO: Sorting table with hits (be patient!). [2020-05-16 10:35:30] INFO: Sequence similarity results written to: out/similarity [2020-05-16 10:35:30] INFO: Calculating length of genes. [2020-05-16 10:35:30] INFO: Indexing sorted hit table. [2020-05-16 10:35:30] INFO: Calculating AAI between all 0 pairs of genomes: [2020-05-16 10:35:30] WARNING: No genome pairs identified.

Unexpected error: <class 'TypeError'> Traceback (most recent call last): File "/home/dikshyant/anaconda3/bin/comparem", line 377, in parser.parse_options(args) File "/home/dikshyant/anaconda3/lib/python3.7/site-packages/comparem/main.py", line 465, in parse_options self.aai(options) File "/home/dikshyant/anaconda3/lib/python3.7/site-packages/comparem/main.py", line 202, in aai options.output_dir) TypeError: cannot unpack non-iterable NoneType object

How do I solve it?

donovan-h-parks commented 4 years ago

Perhaps this is an issue with the sort command. What flavour of Linux are you using? See the note at the top of the CompareM README file: https://github.com/dparks1134/CompareM