It appears that CoPTR completed successfully (as indicated by the log), but the output file (out.csv) is empty. Could you help me troubleshoot where the problem might be?
[INFO] [Aug 13, 2025 13:22:11] [coptr.bam_processor] Processing ./results/bam/AAB-S01R1/AAB-S01R1.bam.
[INFO] [Aug 13, 2025 13:43:22] [coptr.bam_processor] Determining reference genomes.
[INFO] [Aug 13, 2025 13:53:53] [coptr.bam_processor] Collecting multi-mapped reads.
[INFO] [Aug 13, 2025 14:12:08] [coptr.bam_processor] Assigning multi-mapped reads.
[INFO] [Aug 13, 2025 15:38:38] [coptr.bam_processor] Grouping reads by reference genome.
[INFO] [Aug 13, 2025 15:38:56] [coptr.cli] Found 579298 reference sequences corresponding to 1475 genomes.
[INFO] [Aug 13, 2025 15:39:14] [coptr.cli] Grouping reads by reference genome.
[INFO] [Aug 13, 2025 15:39:14] [coptr.cli] Saving to ./results/coverage-maps/coverage-maps-genome:
[INFO] [Aug 13, 2025 15:39:14] [coptr.cli] AAB-S01R1.cm.pkl
[INFO] [Aug 13, 2025 15:39:18] [coptr.cli] Grouping by reference genome: Complete.
[INFO] [Aug 13, 2025 15:39:18] [coptr.cli] The --restart flag can be used to start from here.
[INFO] [Aug 13, 2025 15:39:18] [coptr.coptr_ref] Checking reference genomes.
[INFO] [Aug 13, 2025 15:39:18] [coptr.coptr_contig] Checking reference genomes.
[INFO] [Aug 13, 2025 15:39:44] [coptr.cli] Writing ./results/out.csv.
[INFO] [Aug 13, 2025 15:39:44] [coptr.cli] Done.
[INFO] [Aug 13, 2025 15:39:44] [coptr.cli] You may now remove the folder ./results/coverage-maps/coverage-maps-genome.
It appears that CoPTR completed successfully (as indicated by the log), but the output file (out.csv) is empty. Could you help me troubleshoot where the problem might be?
[INFO] [Aug 13, 2025 13:22:11] [coptr.bam_processor] Processing ./results/bam/AAB-S01R1/AAB-S01R1.bam.
[INFO] [Aug 13, 2025 13:43:22] [coptr.bam_processor] Determining reference genomes.
[INFO] [Aug 13, 2025 13:53:53] [coptr.bam_processor] Collecting multi-mapped reads.
[INFO] [Aug 13, 2025 14:12:08] [coptr.bam_processor] Assigning multi-mapped reads.
[INFO] [Aug 13, 2025 15:38:38] [coptr.bam_processor] Grouping reads by reference genome.
[INFO] [Aug 13, 2025 15:38:56] [coptr.cli] Found 579298 reference sequences corresponding to 1475 genomes.
[INFO] [Aug 13, 2025 15:39:14] [coptr.cli] Grouping reads by reference genome.
[INFO] [Aug 13, 2025 15:39:14] [coptr.cli] Saving to ./results/coverage-maps/coverage-maps-genome:
[INFO] [Aug 13, 2025 15:39:14] [coptr.cli] AAB-S01R1.cm.pkl
[INFO] [Aug 13, 2025 15:39:18] [coptr.cli] Grouping by reference genome: Complete.
[INFO] [Aug 13, 2025 15:39:18] [coptr.cli] The --restart flag can be used to start from here.
[INFO] [Aug 13, 2025 15:39:18] [coptr.coptr_ref] Checking reference genomes.
[INFO] [Aug 13, 2025 15:39:18] [coptr.coptr_contig] Checking reference genomes.
[INFO] [Aug 13, 2025 15:39:44] [coptr.cli] Writing ./results/out.csv.
[INFO] [Aug 13, 2025 15:39:44] [coptr.cli] Done.
[INFO] [Aug 13, 2025 15:39:44] [coptr.cli] You may now remove the folder ./results/coverage-maps/coverage-maps-genome.