Hi,
I would like to analyze the similarity of a set of genome sequence (Vibrio stains) with mercat2's approach.
I installed mercat2 with mamba as instructed in the repository (using Python 3.10.14), and runned as follows.
I noticed the error happen only when multi sample (2โฅ) were supplied to the program.
How should I deal with this ?
best,
=============================================================================
$ cp GCF*fna test/
$ mercat2.py -f test/ -k 3 -n 8 -c 10
.
.
...
GCF_024442235.1 .fna
GCF_028743655.1 .fna
GCF_025917725.1 .fna
GCF_003691505.1 .fna
GCF_009665315.1 .fna
GCF_003691545.1 .fna
GCF_001310575.2 .fna
GCF_022453845.1 .fna
GCF_002887655.1 .fna
GCF_002021755.1 .fna
Time to load 16 files: 8.51 seconds
Checking for large nucleotide files
Processing Nucleotides
Running Mercat2 using 18 cores
Time to count 3-mers: 1.71 seconds
Creating Nucleotide Graphs
/home/kazu/mambaforge/envs/mercat2/lib/python3.10/site-packages/sklearn/metrics/pairwise.py:2317: DataConversionWarning:
Data was converted to boolean for metric dice
/home/kazu/mambaforge/envs/mercat2/lib/python3.10/site-packages/sklearn/metrics/pairwise.py:2317: DataConversionWarning:
Data was converted to boolean for metric jaccard
Error with beta metric: Mahalanobis
Data must be symmetric and cannot contain NaNs.
/home/kazu/mambaforge/envs/mercat2/lib/python3.10/site-packages/sklearn/metrics/pairwise.py:2317: DataConversionWarning:
Data was converted to boolean for metric matching
/home/kazu/mambaforge/envs/mercat2/lib/python3.10/site-packages/sklearn/metrics/pairwise.py:2317: DataConversionWarning:
Data was converted to boolean for metric rogerstanimoto
/home/kazu/mambaforge/envs/mercat2/lib/python3.10/site-packages/sklearn/metrics/pairwise.py:2317: DataConversionWarning:
Data was converted to boolean for metric russellrao
/home/kazu/mambaforge/envs/mercat2/lib/python3.10/site-packages/sklearn/metrics/pairwise.py:2317: DataConversionWarning:
Data was converted to boolean for metric sokalmichener
/home/kazu/mambaforge/envs/mercat2/lib/python3.10/site-packages/sklearn/metrics/pairwise.py:2317: DataConversionWarning:
Data was converted to boolean for metric sokalsneath
/home/kazu/mambaforge/envs/mercat2/lib/python3.10/site-packages/sklearn/metrics/pairwise.py:2317: DataConversionWarning:
Data was converted to boolean for metric yule
Gathering Diversity Metrics
Traceback (most recent call last):
File "/home/kazu/mambaforge/envs/mercat2/bin/mercat2.py", line 508, in
mercat_main()
File "/home/kazu/mambaforge/envs/mercat2/bin/mercat2.py", line 499, in mercat_main
mercat2_report.merge_tsv(tomerge, outfile)
File "/home/kazu/mambaforge/envs/mercat2/lib/python3.10/site-packages/mercat2_lib/mercat2_report.py", line 128, in merge_tsv
kmer = sorted(kmers)[0]
IndexError: list index out of range