[2026-06-08T08:34:03] Launching Arriba 2.4.0
[2026-06-08T08:34:03] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:34:12] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:34:16] Reading chimeric alignments from 'aih-tih-sc-58b830-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9755872)
[2026-06-08T08:39:11] Marking multi-mapping alignments (marked=6540217)
[2026-06-08T08:39:15] Detecting strandedness (reverse)
[2026-06-08T08:39:15] Assigning strands to alignments 
[2026-06-08T08:39:18] Annotating alignments 
[2026-06-08T08:39:53] Filtering duplicates (remaining=2688937)
[2026-06-08T08:39:57] 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=2475888)
[2026-06-08T08:39:59] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2475888)
[2026-06-08T08:40:01] Filtering viral contigs with expression lower than the top 5 (remaining=2475888)
[2026-06-08T08:40:06] Filtering viral contigs with less than 5% coverage (remaining=2475888)
[2026-06-08T08:40:08] Estimating fragment length (mate gap mean=-85.0049, mate gap stddev=26.9251, read length mean=120.273)
[2026-06-08T08:40:08] Filtering read-through fragments with a distance <=10000bp (remaining=2346704)
[2026-06-08T08:40:10] Filtering inconsistently clipped mates (remaining=2296502)
[2026-06-08T08:40:12] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2203158)
[2026-06-08T08:40:15] Filtering fragments with small insert size (remaining=2202435)
[2026-06-08T08:40:17] Filtering alignments with long gaps (remaining=2202435)
[2026-06-08T08:40:19] Filtering fragments with both mates in the same gene (remaining=2201716)
[2026-06-08T08:40:21] Filtering fusions arising from hairpin structures (remaining=2091635)
[2026-06-08T08:40:23] Filtering reads with a mismatch p-value <=0.01 (remaining=786514)
[2026-06-08T08:40:30] Filtering reads with low entropy (k-mer content >=60%) (remaining=308319)
[2026-06-08T08:40:36] Finding fusions and counting supporting reads (total=279847)
[2026-06-08T08:40:49] Merging adjacent fusion breakpoints (remaining=277541)
[2026-06-08T08:40:50] Filtering multi-mapping fusions by alignment score and read support (remaining=147584)
[2026-06-08T08:41:23] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:27] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=146803)
[2026-06-08T08:41:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=88774)
[2026-06-08T08:41:28] Filtering fusions with <2 supporting reads (remaining=8529)
[2026-06-08T08:41:28] Filtering fusions with an e-value >=0.3 (remaining=1982)
[2026-06-08T08:41:29] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2014)
[2026-06-08T08:41:32] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1968)
[2026-06-08T08:41:32] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1968)
[2026-06-08T08:41:33] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1907)
[2026-06-08T08:41:36] Searching for fusions with spliced split reads (remaining=2012)
[2026-06-08T08:41:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=1520)
[2026-06-08T08:41:41] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1497)
[2026-06-08T08:41:41] Searching for fusions with >=4 spliced events (remaining=1660)
[2026-06-08T08:41:42] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=556)
[2026-06-08T08:41:54] Filtering fusions with anchors <=23nt (remaining=477)
[2026-06-08T08:41:54] Filtering end-to-end fusions with low support (remaining=457)
[2026-06-08T08:41:55] Filtering fusions with no coverage around the breakpoints (remaining=440)
[2026-06-08T08:41:55] Indexing gene sequences 
[2026-06-08T08:41:57] Filtering genes with >=30% identity (remaining=158)
[2026-06-08T08:41:58] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=94)
[2026-06-08T08:42:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=91)
[2026-06-08T08:42:00] Searching for additional isoforms (remaining=101)
[2026-06-08T08:42:01] Assigning confidence scores to events 
[2026-06-08T08:42:03] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:42:03] Writing fusions to file 'aih-tih-sc-58b830-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:42:04] Writing discarded fusions to file 'aih-tih-sc-58b830-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:19] Freeing resources
[2026-06-08T08:42:34] Done (elapsed time=00:08:31, CPU time=00:08:30, peak memory=14.1gb)