[2026-06-03T20:17:07] Launching Arriba 2.4.0
[2026-06-03T20:17:07] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:17:16] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:17:19] Reading chimeric alignments from 'aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9861306)
[2026-06-03T20:24:05] Marking multi-mapping alignments (marked=6405148)
[2026-06-03T20:24:09] Detecting strandedness (reverse)
[2026-06-03T20:24:09] Assigning strands to alignments 
[2026-06-03T20:24:11] Annotating alignments 
[2026-06-03T20:24:44] Filtering duplicates (remaining=6859113)
[2026-06-03T20:24:51] 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=6419857)
[2026-06-03T20:24:53] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6419857)
[2026-06-03T20:24:55] Filtering viral contigs with expression lower than the top 5 (remaining=6419857)
[2026-06-03T20:24:59] Filtering viral contigs with less than 5% coverage (remaining=6419857)
[2026-06-03T20:25:02] Estimating fragment length (mate gap mean=-85.3661, mate gap stddev=30.3476, read length mean=133.063)
[2026-06-03T20:25:02] Filtering read-through fragments with a distance <=10000bp (remaining=6049207)
[2026-06-03T20:25:04] Filtering inconsistently clipped mates (remaining=5928513)
[2026-06-03T20:25:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5761488)
[2026-06-03T20:25:10] Filtering fragments with small insert size (remaining=5760668)
[2026-06-03T20:25:12] Filtering alignments with long gaps (remaining=5760667)
[2026-06-03T20:25:14] Filtering fragments with both mates in the same gene (remaining=5759293)
[2026-06-03T20:25:16] Filtering fusions arising from hairpin structures (remaining=5334284)
[2026-06-03T20:25:19] Filtering reads with a mismatch p-value <=0.01 (remaining=2457410)
[2026-06-03T20:25:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=1140079)
[2026-06-03T20:25:43] Finding fusions and counting supporting reads (total=879621)
[2026-06-03T20:25:59] Merging adjacent fusion breakpoints (remaining=872742)
[2026-06-03T20:26:01] Filtering multi-mapping fusions by alignment score and read support (remaining=566771)
[2026-06-03T20:26:32] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:26:39] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=564039)
[2026-06-03T20:26:40] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=338942)
[2026-06-03T20:26:41] Filtering fusions with <2 supporting reads (remaining=41087)
[2026-06-03T20:26:42] Filtering fusions with an e-value >=0.3 (remaining=14791)
[2026-06-03T20:26:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14845)
[2026-06-03T20:26:47] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14758)
[2026-06-03T20:26:48] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14759)
[2026-06-03T20:26:49] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8637)
[2026-06-03T20:26:54] Searching for fusions with spliced split reads (remaining=8654)
[2026-06-03T20:26:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=4841)
[2026-06-03T20:27:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4771)
[2026-06-03T20:27:02] Searching for fusions with >=4 spliced events (remaining=5781)
[2026-06-03T20:27:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2299)
[2026-06-03T20:27:18] Filtering fusions with anchors <=23nt (remaining=1820)
[2026-06-03T20:27:19] Filtering end-to-end fusions with low support (remaining=1753)
[2026-06-03T20:27:20] Filtering fusions with no coverage around the breakpoints (remaining=1702)
[2026-06-03T20:27:21] Indexing gene sequences 
[2026-06-03T20:27:27] Filtering genes with >=30% identity (remaining=548)
[2026-06-03T20:27:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=288)
[2026-06-03T20:27:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=239)
[2026-06-03T20:27:39] Searching for additional isoforms (remaining=320)
[2026-06-03T20:27:40] Assigning confidence scores to events 
[2026-06-03T20:27:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:27:44] Writing fusions to file 'aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:27:48] Writing discarded fusions to file 'aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:28:18] Freeing resources
[2026-06-03T20:28:34] Done (elapsed time=00:11:27, CPU time=00:11:26, peak memory=14.8gb)