[2026-06-03T20:14:00] Launching Arriba 2.4.0
[2026-06-03T20:14:00] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:14:13] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:14:17] Reading chimeric alignments from 'aih-tih-sc-d963a2-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11750201)
[2026-06-03T20:23:10] Marking multi-mapping alignments (marked=8131391)
[2026-06-03T20:23:15] Detecting strandedness (reverse)
[2026-06-03T20:23:15] Assigning strands to alignments 
[2026-06-03T20:23:17] Annotating alignments 
[2026-06-03T20:23:55] Filtering duplicates (remaining=7365464)
[2026-06-03T20:24:04] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=6813519)
[2026-06-03T20:24:06] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6813519)
[2026-06-03T20:24:08] Filtering viral contigs with expression lower than the top 5 (remaining=6813519)
[2026-06-03T20:24:14] Filtering viral contigs with less than 5% coverage (remaining=6813519)
[2026-06-03T20:24:17] Estimating fragment length (mate gap mean=-83.9906, mate gap stddev=30.3525, read length mean=130.155)
[2026-06-03T20:24:17] Filtering read-through fragments with a distance <=10000bp (remaining=6395122)
[2026-06-03T20:24:19] Filtering inconsistently clipped mates (remaining=6268831)
[2026-06-03T20:24:22] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6081445)
[2026-06-03T20:24:27] Filtering fragments with small insert size (remaining=6080298)
[2026-06-03T20:24:30] Filtering alignments with long gaps (remaining=6080298)
[2026-06-03T20:24:32] Filtering fragments with both mates in the same gene (remaining=6079135)
[2026-06-03T20:24:35] Filtering fusions arising from hairpin structures (remaining=5661648)
[2026-06-03T20:24:38] Filtering reads with a mismatch p-value <=0.01 (remaining=2566186)
[2026-06-03T20:24:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=1105305)
[2026-06-03T20:25:07] Finding fusions and counting supporting reads (total=876004)
[2026-06-03T20:25:26] Merging adjacent fusion breakpoints (remaining=867790)
[2026-06-03T20:25:28] Filtering multi-mapping fusions by alignment score and read support (remaining=518824)
[2026-06-03T20:26:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:26:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=514659)
[2026-06-03T20:26:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=308190)
[2026-06-03T20:26:11] Filtering fusions with <2 supporting reads (remaining=33864)
[2026-06-03T20:26:11] Filtering fusions with an e-value >=0.3 (remaining=12805)
[2026-06-03T20:26:12] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12883)
[2026-06-03T20:26:16] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12758)
[2026-06-03T20:26:16] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12758)
[2026-06-03T20:26:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6731)
[2026-06-03T20:26:23] Searching for fusions with spliced split reads (remaining=6870)
[2026-06-03T20:26:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=4018)
[2026-06-03T20:26:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3971)
[2026-06-03T20:26:30] Searching for fusions with >=4 spliced events (remaining=4732)
[2026-06-03T20:26:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1976)
[2026-06-03T20:26:50] Filtering fusions with anchors <=23nt (remaining=1494)
[2026-06-03T20:26:50] Filtering end-to-end fusions with low support (remaining=1439)
[2026-06-03T20:26:51] Filtering fusions with no coverage around the breakpoints (remaining=1402)
[2026-06-03T20:26:51] Indexing gene sequences 
[2026-06-03T20:26:58] Filtering genes with >=30% identity (remaining=397)
[2026-06-03T20:27:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=173)
[2026-06-03T20:27:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=149)
[2026-06-03T20:27:03] Searching for additional isoforms (remaining=198)
[2026-06-03T20:27:05] Assigning confidence scores to events 
[2026-06-03T20:27:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:27:08] Writing fusions to file 'aih-tih-sc-d963a2-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:27:10] Writing discarded fusions to file 'aih-tih-sc-d963a2-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:27:41] Freeing resources
[2026-06-03T20:28:01] Done (elapsed time=00:14:01, CPU time=00:14:00, peak memory=16.7gb)