[2026-06-03T20:03:34] Launching Arriba 2.4.0
[2026-06-03T20:03:34] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:03:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:03:58] Reading chimeric alignments from 'aih-tih-sc-92d360-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10063397)
[2026-06-03T20:13:12] Marking multi-mapping alignments (marked=7034763)
[2026-06-03T20:13:17] Detecting strandedness (reverse)
[2026-06-03T20:13:17] Assigning strands to alignments 
[2026-06-03T20:13:19] Annotating alignments 
[2026-06-03T20:13:58] Filtering duplicates (remaining=5070387)
[2026-06-03T20:14:05] 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=4768707)
[2026-06-03T20:14:08] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4768707)
[2026-06-03T20:14:10] Filtering viral contigs with expression lower than the top 5 (remaining=4768707)
[2026-06-03T20:14:14] Filtering viral contigs with less than 5% coverage (remaining=4768707)
[2026-06-03T20:14:17] Estimating fragment length (mate gap mean=-80.7327, mate gap stddev=27.4819, read length mean=117.746)
[2026-06-03T20:14:17] Filtering read-through fragments with a distance <=10000bp (remaining=4457819)
[2026-06-03T20:14:19] Filtering inconsistently clipped mates (remaining=4340399)
[2026-06-03T20:14:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4204043)
[2026-06-03T20:14:25] Filtering fragments with small insert size (remaining=4202774)
[2026-06-03T20:14:27] Filtering alignments with long gaps (remaining=4202774)
[2026-06-03T20:14:29] Filtering fragments with both mates in the same gene (remaining=4201673)
[2026-06-03T20:14:31] Filtering fusions arising from hairpin structures (remaining=3907055)
[2026-06-03T20:14:34] Filtering reads with a mismatch p-value <=0.01 (remaining=1559610)
[2026-06-03T20:14:44] Filtering reads with low entropy (k-mer content >=60%) (remaining=743160)
[2026-06-03T20:14:53] Finding fusions and counting supporting reads (total=621016)
[2026-06-03T20:15:11] Merging adjacent fusion breakpoints (remaining=613727)
[2026-06-03T20:15:13] Filtering multi-mapping fusions by alignment score and read support (remaining=351555)
[2026-06-03T20:15:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:15:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=350458)
[2026-06-03T20:15:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=199401)
[2026-06-03T20:15:58] Filtering fusions with <2 supporting reads (remaining=18793)
[2026-06-03T20:15:59] Filtering fusions with an e-value >=0.3 (remaining=4072)
[2026-06-03T20:15:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4133)
[2026-06-03T20:16:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4049)
[2026-06-03T20:16:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4049)
[2026-06-03T20:16:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3920)
[2026-06-03T20:16:10] Searching for fusions with spliced split reads (remaining=3974)
[2026-06-03T20:16:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=2831)
[2026-06-03T20:16:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2805)
[2026-06-03T20:16:18] Searching for fusions with >=4 spliced events (remaining=3333)
[2026-06-03T20:16:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1429)
[2026-06-03T20:16:39] Filtering fusions with anchors <=23nt (remaining=1218)
[2026-06-03T20:16:39] Filtering end-to-end fusions with low support (remaining=1190)
[2026-06-03T20:16:40] Filtering fusions with no coverage around the breakpoints (remaining=1171)
[2026-06-03T20:16:41] Indexing gene sequences 
[2026-06-03T20:16:48] Filtering genes with >=30% identity (remaining=397)
[2026-06-03T20:16:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=197)
[2026-06-03T20:16:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=132)
[2026-06-03T20:16:56] Searching for additional isoforms (remaining=173)
[2026-06-03T20:16:57] Assigning confidence scores to events 
[2026-06-03T20:17:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:17:01] Writing fusions to file 'aih-tih-sc-92d360-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:17:02] Writing discarded fusions to file 'aih-tih-sc-92d360-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:17:36] Freeing resources
[2026-06-03T20:17:56] Done (elapsed time=00:14:22, CPU time=00:14:21, peak memory=14.7gb)