It appears as though it runs through my samples but I keep getting the following error message with no results at the end, any help would be greatly appreciated:
Generating the k-mer lists:
6 of 6 lists generated.
Counting the k-mers presence frequencies in samples:
6 of 6 samples counted for k-mers presence.
Filtering the k-mers based on their presence frequencies in samples:
100% of 3071453 k-mers filtered.
Building the feature vector from filtered k-mers.
Mapping samples to the feature vector space:
6 of 6 samples mapped.
Converting the set of vectors into data matrix.
6 of 6 vectors inserted into matrix.
Estimating the Mash distances between samples...
Calculating the Gerstein Sonnhammer Coathia weights from mash distance matrix...
Conducting the k-mer specific weighted chi-square tests:
Phage: 100% of 142484 tests conducted.
Filtering the k-mers by p-value:
Phage: 100% of 142484 k-mers filtered.
Conducting the logistic regression analysis of Phage data...
Assembling the k-mers used in regression model of Phage data...
Traceback (most recent call last):
File "/home/cameron/.local/bin/phenotypeseeker", line 209, in
Main()
File "/home/cameron/.local/bin/phenotypeseeker", line 203, in Main
args.func(args)
File "/home/cameron/.local/lib/python2.7/site-packages/PhenotypeSeeker/modeling.py", line 1431, in modeling
headerline
File "/home/cameron/.local/lib/python2.7/site-packages/PhenotypeSeeker/modeling.py", line 1328, in assembling
kmer_assembler(kmers_to_assemble), key = len
File "/home/cameron/.local/lib/python2.7/site-packages/PhenotypeSeeker/modeling.py", line 1254, in kmer_assembler
kmer_length = len(kmer_list[0])
IndexError: list index out of range
It appears as though it runs through my samples but I keep getting the following error message with no results at the end, any help would be greatly appreciated:
Generating the k-mer lists: 6 of 6 lists generated. Counting the k-mers presence frequencies in samples: 6 of 6 samples counted for k-mers presence. Filtering the k-mers based on their presence frequencies in samples: 100% of 3071453 k-mers filtered. Building the feature vector from filtered k-mers. Mapping samples to the feature vector space: 6 of 6 samples mapped. Converting the set of vectors into data matrix. 6 of 6 vectors inserted into matrix. Estimating the Mash distances between samples... Calculating the Gerstein Sonnhammer Coathia weights from mash distance matrix... Conducting the k-mer specific weighted chi-square tests: Phage: 100% of 142484 tests conducted. Filtering the k-mers by p-value: Phage: 100% of 142484 k-mers filtered. Conducting the logistic regression analysis of Phage data... Assembling the k-mers used in regression model of Phage data... Traceback (most recent call last): File "/home/cameron/.local/bin/phenotypeseeker", line 209, in
Main()
File "/home/cameron/.local/bin/phenotypeseeker", line 203, in Main
args.func(args)
File "/home/cameron/.local/lib/python2.7/site-packages/PhenotypeSeeker/modeling.py", line 1431, in modeling
headerline
File "/home/cameron/.local/lib/python2.7/site-packages/PhenotypeSeeker/modeling.py", line 1328, in assembling
kmer_assembler(kmers_to_assemble), key = len
File "/home/cameron/.local/lib/python2.7/site-packages/PhenotypeSeeker/modeling.py", line 1254, in kmer_assembler
kmer_length = len(kmer_list[0])
IndexError: list index out of range