BUG -4294967296 about ultra HOT 8 OPEN

./uLTRA     pipeline     --t 2     --prefix alz.chunk3     --isoseq --disable_infer     ~/Downloads/ultra_bug/Homo_sapiens.GRCh38.dna.chromosome.19.fasta     ~/Downloads/ultra_bug/Homo_sapiens.GRCh38.104.chr.13_18_19.gtf     ~/Downloads/ultra_bug/alz.chunk3_tama.fa     ~/Downloads/ultra_bug/ultra_out

creating /Users/kxs624/Downloads/ultra_bug/ultra_out
total_flanks2: 20352
total_flank_size 20395551
total_unique_segment_counter 7303161
total_segments_bad 5517888
bad 89736
total parts size: 7391334
total exons size: 20040918
min_intron: 1
Number of ref seqs in gff: 15570
Number of ref seqs in fasta: 1
6622546.0 Unique kmers in reference part sequences with abundance > 1
AAAAAAAAAAAAAAAAAAAA 538
TTTTTTTTTTTTTTTTTTTT 496
CCTCCCAAAGTGCTGGGATT 385
GCCTCCCAAAGTGCTGGGAT 382
[...]
ACGGTGAAACCCCGTCTCTA 200
GAGTGCAGTGGCGTGATCTC 200
AAAAAATTAGCCGGGCGTGG 200
CCAAAGTGCTAGGATTACAG 200
CACACCCAGCTAATTTTTGT 200
GATTGCGCCACTGCACTCCA 200
CCAGGAGGTGGAGGTTGCAG 200
11038 11038 out of 20352 sequences has been modified in masking step.
<multiprocessing.context.SpawnContext object at 0x7fc20382c820>
Environment set: <multiprocessing.context.SpawnContext object at 0x7fc20382c820>
Using 2 cores.
Filtering reads aligned to unindexed regions with minimap2 
Done filtering. Reads filtered:21
batch nt: 97383 total_nt: 194765
37
36
Using SLAMEM
Using SLAMEM
Using SLAMEM
Using SLAMEM
Time for slaMEM to find mems:45.91997790336609 seconds.
Starting aligning reads.
Nr reads: 73 nr batches: 2 [37, 36]
READ 37 RECORDS.
READ 37 RECORDS.
Number of instances solved with quadratic collinear chainer solution: 84
Number of instances solved with n*log n collinear chainer solution: 15
READ 36 RECORDS.
READ 36 RECORDS.
Number of instances solved with quadratic collinear chainer solution: 103
Number of instances solved with n*log n collinear chainer solution: 8
Time elapesd multiprocessing: 1.5507452487945557
Time to align reads:1.5510809421539307 seconds.
Time to merge SAM-files:0.00915384292602539 seconds.
21 reads were not attempted to be aligned with ultra, instead alternative aligner was used.
6 reads with primary alignments were replaced with alternative aligner because they were unaligned with uLTRA.
1 primary alignments had best fit with uLTRA.
4 primary alignments had equal fit.
3 primary alignments had best fit with alternative aligner.
Table of score-difference between alignment methods (negative number: alternative aligner better fit, positive number is uLTRA better fit)
Score is calculated as sum(identities) - sum(ins, del, subs)
Format: Score difference: Number of primary alignments 
[-4294967296 - -100): 2
[-100 - -50): 0
[-50 - -20): 1
[-20 - -10): 0
[-10 - -5): 0
[-5 - -4): 0
[-4 - -3): 0
[-3 - -2): 0
[-2 - -1): 0
[-1 - 0): 0
[0 - 1): 4
[1 - 2): 0
[2 - 3): 0
[3 - 4): 0
[4 - 5): 0
[5 - 10): 0
[10 - 20): 0
[20 - 50): 0
[50 - 100): 0
[100 - 4294967296): 1
defaultdict(<class 'int'>, {'unaligned': 65, 'FSM': 4, 'NO_SPLICE': 2, 'Insufficient_junction_coverage_unclassified': 1, 'NIC_novel': 1})
total alignment coverage: 7.350311311286634
Deleting temporary files...
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/seeds_batch_0_rc.txt
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/seeds_batch_1.txt
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/seeds_batch_0.txt
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/seeds_batch_1_rc.txt
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/slamem_stdout_1.1
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/slamem_stderr_0_rc.1
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/slamem_stderr_0.1
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/slamem_stderr_1_rc.1
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/slamem_stdout_0_rc.1
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/slamem_stderr_1.1
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/slamem_stdout_1_rc.1
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/slamem_stdout_0.1
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/reads_batch_0.fa
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/reads_batch_1_rc.fa
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/reads_batch_1.fa
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/reads_batch_0.sam
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/reads_batch_1.sam
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/reads_batch_0_rc.fa
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/minimap2.sam
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/minimap2_errors.1
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/uLTRA_batch_0.stderr
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/uLTRA_batch_1.stderr
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/reads_after_genomic_filtering.fasta
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/indexed.sam
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/unindexed.sam
removed: /Users/kxs624/Downloads/ultra_bug/ultra_out/refs_sequences.fa
Done.