Patch overflow with high BAM coverage

[RenzoTale88]

Hi,
I tried to run ragtag correct with a BAM file with the following command line:

ragtag.py correct \
        -R $READS \
        -T corr \
        -j ragtag_skip.txt \
        -t $SLURM_CPUS_PER_TASK \
        --aligner $( which nucmer ) \
        --nucmer-params '--maxmatch -l 100 -c 500 -t'"$SLURM_CPUS_PER_TASK"'' \
        -o $DNAME \
        $REF \
        $FASTA

This returned me the following log:

Fri Aug 28 10:39:35 2026 --- VERSION: RagTag v2.1.0
Fri Aug 28 10:39:35 2026 --- CMD: ragtag.py correct -R HOSTILE/rob1_29.clean.fasta.gz -T corr -j ragtag_skip.txt -t 32 --aligner /mnt/envs/ragtag/bin/nucmer --nucmer-params --maxmatch -l 100 -c 500 -t32 -o RAGTAG_FINAL_CORRECT/p_ctg/ REF/GCF_002263795.3_ARS-UCD2.0_genomic.fna FINAL/p_ctg.final.purged.fa
Fri Aug 28 10:39:35 2026 --- WARNING: Without '-u' invoked, some component/object AGP pairs might share the same ID. Some external programs/databases don't like this. To ensure valid AGP format, use '-u'.
Fri Aug 28 10:39:35 2026 --- INFO: Mapping the query genome to the reference genome
Fri Aug 28 10:39:35 2026 --- INFO: Running: /mnt/envs/ragtag/bin/nucmer --maxmatch -l 100 -c 500 -t32 -p /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.asm /mnt/REF/GCF_002263795.3_ARS-UCD2.0_genomic.fna /mnt/FINAL/p_ctg.final.purged.fa 2> /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.asm.delta.log
Fri Aug 28 18:30:41 2026 --- INFO: Finished running : /mnt/envs/ragtag/bin/nucmer --maxmatch -l 100 -c 500 -t32 -p /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.asm /mnt/REF/GCF_002263795.3_ARS-UCD2.0_genomic.fna /mnt/FINAL/p_ctg.final.purged.fa > /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.asm.delta.log
Fri Aug 28 18:30:41 2026 --- INFO: Running: ragtag_delta2paf.py /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.asm.delta > /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.asm.paf 2> /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.err
Fri Aug 28 18:42:19 2026 --- INFO: Finished running : ragtag_delta2paf.py /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.asm.delta > /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.asm.paf 2> /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.err
Fri Aug 28 18:42:19 2026 --- INFO: Reading whole genome alignments
Fri Aug 28 18:43:28 2026 --- INFO: Filtering and merging alignments
Fri Aug 28 18:44:28 2026 --- INFO: Validating putative query breakpoints via read alignment
Fri Aug 28 18:44:28 2026 --- INFO: Aligning reads to query sequences
Fri Aug 28 18:44:28 2026 --- INFO: Running: minimap2 -ax asm20 -t 32 /mnt/FINAL/p_ctg.final.purged.fa /mnt/HOSTILE/rob1_29.clean.fasta.gz > /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.reads.sam 2> /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.reads.sam.log
Fri Aug 28 21:10:02 2026 --- INFO: Finished running : minimap2 -ax asm20 -t 32 /mnt/FINAL/p_ctg.final.purged.fa /mnt/HOSTILE/rob1_29.clean.fasta.gz > /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.reads.sam 2> /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.reads.sam.log
Fri Aug 28 21:10:02 2026 --- INFO: Compressing, sorting, and indexing read alignments
Fri Aug 28 21:23:20 2026 --- INFO: Indexing read alignments
Fri Aug 28 21:29:07 2026 --- INFO: Validating putative query breakpoints
Fri Aug 28 21:29:07 2026 --- INFO: Calculating global read coverage
/mnt/envs/ragtag/bin/ragtag_correct.py:119: RuntimeWarning: overflow encountered in scalar add
  mid = sum(covs) // 2
Fri Aug 28 22:51:51 2026 --- INFO: The global median read coverage is 0X
Fri Aug 28 22:51:51 2026 --- INFO: The max and min coverage thresholds are 0X and 5X, respectively
Fri Aug 28 22:54:48 2026 --- INFO: Writing: /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.agp
Fri Aug 28 22:54:48 2026 --- INFO: Writing broken contigs
Fri Aug 28 22:54:48 2026 --- INFO: Running: ragtag_break_query.py /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.agp /mnt/FINAL/p_ctg.final.purged.fa > /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.fasta 2> /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.err
Fri Aug 28 22:54:54 2026 --- INFO: Finished running : ragtag_break_query.py /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.agp /mnt/FINAL/p_ctg.final.purged.fa > /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.fasta 2> /mnt/RAGTAG_FINAL_CORRECT/p_ctg/ragtag.correct.err
Fri Aug 28 22:54:54 2026 --- INFO: Goodbye

This causes an overflow due to the use of np.int32 here. Using np.int64 fixes the problem.