Found complete reference genome with <500bp. This is probably due to a mislabeled contig.

[ykm7788]

Hiya, when I was running coptr estimate map out.csv --min-reads 2500, I got this error:

[INFO] [Oct 25, 2024 11:03:58] [coptr.cli] Grouping reads by reference genome.
[INFO] [Oct 25, 2024 11:03:58] [coptr.cli] Saving to map/coverage-maps-genome:
[INFO] [Oct 25, 2024 11:03:58] [coptr.cli] sample1.pkl
[INFO] [Oct 25, 2024 11:05:59] [coptr.cli] sample2.pkl
[INFO] [Oct 25, 2024 11:07:52] [coptr.cli] sample3.pkl
[INFO] [Oct 25, 2024 11:09:39] [coptr.cli] Grouping by reference genome: Complete.
[INFO] [Oct 25, 2024 11:09:39] [coptr.cli] The --restart flag can be used to start from here.
[INFO] [Oct 25, 2024 11:09:39] [coptr.coptr_ref] Checking reference genomes.
[INFO] [Oct 25, 2024 11:09:59] [coptr.coptr_ref] Running 1007104.3.patric|accn|AFGG01000001.
[INFO] [Oct 25, 2024 11:10:03] [coptr.coptr_ref] Finished 1007104.3.patric|accn|AFGG01000001.
[INFO] [Oct 25, 2024 11:10:27] [coptr.coptr_ref] Running 1007104.3.patric|accn|AFGG01000002.
[INFO] [Oct 25, 2024 11:10:29] [coptr.coptr_ref] Finished 1007104.3.patric|accn|AFGG01000002.
[INFO] [Oct 25, 2024 11:10:50] [coptr.coptr_ref] Running 1007104.3.patric|accn|AFGG01000003.
[INFO] [Oct 25, 2024 11:10:52] [coptr.coptr_ref] Finished 1007104.3.patric|accn|AFGG01000003.
[INFO] [Oct 25, 2024 11:11:17] [coptr.coptr_ref] Running 1007104.3.patric|accn|AFGG01000004.
[INFO] [Oct 25, 2024 11:11:19] [coptr.coptr_ref] Finished 1007104.3.patric|accn|AFGG01000004.
[INFO] [Oct 25, 2024 11:11:41] [coptr.coptr_ref] Running 1007104.3.patric|accn|AFGG01000005.
[INFO] [Oct 25, 2024 11:11:42] [coptr.coptr_ref] Finished 1007104.3.patric|accn|AFGG01000005.
[INFO] [Oct 25, 2024 11:12:03] [coptr.coptr_ref] Running 1007104.3.patric|accn|AFGG01000006.
[INFO] [Oct 25, 2024 11:12:05] [coptr.coptr_ref] Finished 1007104.3.patric|accn|AFGG01000006.
[INFO] [Oct 25, 2024 11:12:31] [coptr.coptr_ref] Running 1007104.3.patric|accn|AFGG01000008.
[INFO] [Oct 25, 2024 11:12:33] [coptr.coptr_ref] Finished 1007104.3.patric|accn|AFGG01000008.
[INFO] [Oct 25, 2024 11:13:06] [coptr.coptr_ref] Running 1007104.3.patric|accn|AFGG01000010.
[INFO] [Oct 25, 2024 11:13:08] [coptr.coptr_ref] Finished 1007104.3.patric|accn|AFGG01000010.
[INFO] [Oct 25, 2024 11:13:38] [coptr.coptr_ref] Running 1007104.3.patric|accn|AFGG01000011.
[INFO] [Oct 25, 2024 11:13:39] [coptr.coptr_ref] Finished 1007104.3.patric|accn|AFGG01000011.
[INFO] [Oct 25, 2024 11:14:05] [coptr.coptr_ref] Running 1007104.3.patric|accn|AFGG01000012.
[INFO] [Oct 25, 2024 11:14:07] [coptr.coptr_ref] Finished 1007104.3.patric|accn|AFGG01000012.
[INFO] [Oct 25, 2024 11:14:33] [coptr.coptr_ref] Running 1007104.3.patric|accn|AFGG01000014.
[INFO] [Oct 25, 2024 11:14:34] [coptr.coptr_ref] Finished 1007104.3.patric|accn|AFGG01000014.
[INFO] [Oct 25, 2024 11:15:16] [coptr.coptr_ref] Running 1007104.3.patric|accn|AFGG01000016.
[INFO] [Oct 25, 2024 11:15:17] [coptr.coptr_ref] Finished 1007104.3.patric|accn|AFGG01000016.
[INFO] [Oct 25, 2024 11:15:49] [coptr.coptr_ref] Running 1007104.3.patric|accn|AFGG01000017.
[INFO] [Oct 25, 2024 11:15:50] [coptr.coptr_ref] Finished 1007104.3.patric|accn|AFGG01000017.
[INFO] [Oct 25, 2024 11:16:16] [coptr.coptr_ref] Running 1007104.3.patric|accn|AFGG01000021.
[INFO] [Oct 25, 2024 11:16:17] [coptr.coptr_ref] Finished 1007104.3.patric|accn|AFGG01000021.
[INFO] [Oct 25, 2024 11:16:39] [coptr.coptr_ref] Running 1007104.3.patric|accn|AFGG01000022.
[INFO] [Oct 25, 2024 11:16:40] [coptr.coptr_ref] Finished 1007104.3.patric|accn|AFGG01000022.
[ERROR] [Oct 25, 2024 11:16:40] [coptr.coptr_ref] Found complete reference genome with <500bp. This is probably due to a mislabeled contig. Please check your .genomes file.
Traceback (most recent call last):
File "/home/ykm/software/conda/envs/coptr/bin/coptr", line 8, in
sys.exit(cli())
File "/home/ykm/software/conda/envs/coptr/lib/python3.7/site-packages/coptr/cli.py", line 576, in cli
ProgramOptions()
File "/home/ykm/software/conda/envs/coptr/lib/python3.7/site-packages/coptr/cli.py", line 70, in init
getattr(self, args.command)()
File "/home/ykm/software/conda/envs/coptr/lib/python3.7/site-packages/coptr/cli.py", line 387, in estimate
plot_folder=args.plot,
File "/home/ykm/software/conda/envs/coptr/lib/python3.7/site-packages/coptr/coptr_ref.py", line 1061, in estimate_ptrs_coptr_ref
coptr_ref_estimates[ref_id] = coptr_ref.estimate_ptrs(coverage_maps)
File "/home/ykm/software/conda/envs/coptr/lib/python3.7/site-packages/coptr/coptr_ref.py", line 850, in estimate_ptrs
cm.read_positions, cm.length
File "/home/ykm/software/conda/envs/coptr/lib/python3.7/site-packages/coptr/coptr_ref.py", line 117, in filter_reads
read_positions, genome_length, bin_size
File "/home/ykm/software/conda/envs/coptr/lib/python3.7/site-packages/coptr/coptr_ref.py", line 364, in filter_reads_phase1
binned_reads = self.bin_reads(read_positions, genome_length, bin_size)
File "/home/ykm/software/conda/envs/coptr/lib/python3.7/site-packages/coptr/coptr_ref.py", line 491, in bin_reads
nbins = int(math.ceil(genome_length / bin_size))
ZeroDivisionError: float division by zero

For mapping, I used this command coptr extract bam map --ref-genome-regex /home/.opt/bioinfomatics_databases/IGGdb/index/igg and got no error.

I also removed several reference genomes next to the good one (1007104.3.patric|accn|AFGG01000022), but still got this error.