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sufforest / SolidBin

A genome binning method for contig binning, based on semi-supervised spectral clustering method.
GNU General Public License v2.0
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Object of type 'NoneType' has no len() #8

Open ZhangZhenmiao opened 4 years ago

ZhangZhenmiao commented 4 years ago

Hi,

I got an error of "object of type 'NoneType' has no len()" after "finish generating affinity matrix". Can you help me?

2020-09-03 18:00:08,794 - Input arguments: 2020-09-03 18:00:08,914 - contig_file: final.contigs.fa 2020-09-03 18:00:08,914 - coverage_profiles: input_solidbin/coverage_new.tsv 2020-09-03 18:00:08,915 - composition_profiles: kmer_4_f1000.csv 2020-09-03 18:00:08,915 - output path: solidbin_output/solidbin.txt 2020-09-03 18:00:08,915 - priori_ml_list: Not Available 2020-09-03 18:00:08,915 - priori_cl_list: Not Available 2020-09-03 18:00:08,915 - clusters: Auto 2020-09-03 18:00:14,958 - Start generating affinity matrix 2020-09-03 18:00:16,359 - Finish generating affinity matrix exec cmd: /home/comp/zmzhang/software/SolidBin/auxiliary/test_getmarker.pl final.contigs.fa.hmmout final.contigs.fa 1001 final.contigs.fa.seed 0 Traceback (most recent call last): File "/home/comp/zmzhang/software/SolidBin/SolidBin.py", line 738, in bestK=len(seed_list) TypeError: object of type 'NoneType' has no len()

ziyewang commented 4 years ago

Sorry for not making a response in time. It seems your "final.contigs.fa.seed" is empty. This may be caused by two reasons: 1) The contig file doesn't contain single-copy genes; and 2) The FragGeneScan did not work well. I have uploaded some test files and updated the description for generating the input files and installation methods in Readme, and you can test your installation using the files.

Best, Ziye