The output of all_genes.fna is empty.

[gaojingxun]

2024-11-16 04:29:55,788 - INFO - 59 were idenitified with 66 taxids
2024-11-16 04:29:55,789 - INFO - Relative abundance and genome coverage of each species can be found in result/mpg/species_stats.tsv
2024-11-16 04:29:55,789 - INFO - Writing nucleotide sequences of genes
2024-11-16 04:30:03,942 - INFO - Aligning genes to reference genomes
2024-11-16 04:30:18,339 - INFO - Obtaining IDs of reference genomes
2024-11-16 04:30:18,941 - INFO - Obtaining genes mapped to reference genomes
2024-11-16 04:30:18,942 - INFO - Obtaining amino acid sequences of genes mapped
2024-11-16 04:30:19,754 - INFO - Total number of genes: 0
2024-11-16 04:30:19,754 - INFO - Number of genes mapped: 0

1. The above is a log entry. What could be the reason for this, and what caused the output file all_genes.fna to be empty?
2. My command:
   condiga
   -c final.contigs.fa
   -ta Kraken/kraken_result.txt
   -g final.contigs.fa.lst
   -cov contig_coverage.tsv
   -as assembly_summary.txt
   -o result/mpg
3. In the file result/mpg/species_stats.tsv, I see that the relative abundance and genome coverage for some species meet the default requirements, but the all_genes.fna file is still empty.
4. Here are the detailed error messages:
   2024-11-16 04:29:55,789 - INFO - Relative abundance and genome coverage of each species can be found in result/mpg/species_stats.tsv
   2024-11-16 04:29:55,789 - INFO - Writing nucleotide sequences of genes
   2024-11-16 04:30:03,942 - INFO - Aligning genes to reference genomes
   [M::mm_idx_gen::5.1611.36] collected minimizers
   [M::mm_idx_gen::11.9211.00] sorted minimizers
   [M::main::11.9211.00] loaded/built the index for 133 target sequence(s)
   [M::mm_mapopt_update::12.9101.00] mid_occ = 65
   [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 133
   [M::mm_idx_stat::13.655*0.99] distinct minimizers: 29065550 (65.39% are singletons); average occurrences: 2.086; average spacing: 5.360
   [M::main] Version: 2.17-r941
   [M::main] CMD: minimap2 -t 8 result/mpg/Reference_Sequences/refs.fna result/mpg/all_genes.fna
   [M::main] Real time: 13.761 sec; CPU: 13.635 sec; Peak RSS: 2.198 GB
   2024-11-16 04:30:18,339 - INFO - Obtaining IDs of reference genomes
   2024-11-16 04:30:18,941 - INFO - Obtaining genes mapped to reference genomes
   2024-11-16 04:30:18,942 - INFO - Obtaining amino acid sequences of genes mapped
   2024-11-16 04:30:19,754 - INFO - Total number of genes: 0
   2024-11-16 04:30:19,754 - INFO - Number of genes mapped: 0
   Traceback (most recent call last):
   File "/home/ghy/miniconda/miniconda3/envs/condiga/bin/condiga", line 253, in
   main()
   File "/home/ghy/miniconda/miniconda3/envs/condiga/lib/python3.9/site-packages/click/core.py", line 1157, in call
   return self.main(*args, **kwargs)
   File "/home/ghy/miniconda/miniconda3/envs/condiga/lib/python3.9/site-packages/click/core.py", line 1078, in main
   rv = self.invoke(ctx)
   File "/home/ghy/miniconda/miniconda3/envs/condiga/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
   return ctx.invoke(self.callback, **ctx.params)
   File "/home/ghy/miniconda/miniconda3/envs/condiga/lib/python3.9/site-packages/click/core.py", line 783, in invoke
   return __callback(*args, **kwargs)
   File "/home/ghy/miniconda/miniconda3/envs/condiga/bin/condiga", line 227, in main
   logger.info(f"Percentage of genes mapped: {(len(gene_seq)-unmapped_count)/len(gene_seq)}")
   ZeroDivisionError: division by zero