[2026-06-03T20:13:59] Launching Arriba 2.4.0
[2026-06-03T20:13:59] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:14:08] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:14:11] Reading chimeric alignments from 'aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10012914)
[2026-06-03T20:20:48] Marking multi-mapping alignments (marked=6353834)
[2026-06-03T20:20:52] Detecting strandedness (reverse)
[2026-06-03T20:20:52] Assigning strands to alignments 
[2026-06-03T20:20:54] Annotating alignments 
[2026-06-03T20:21:30] Filtering duplicates (remaining=6623256)
[2026-06-03T20:21:38] 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=6296744)
[2026-06-03T20:21:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6296744)
[2026-06-03T20:21:42] Filtering viral contigs with expression lower than the top 5 (remaining=6296744)
[2026-06-03T20:21:47] Filtering viral contigs with less than 5% coverage (remaining=6296744)
[2026-06-03T20:21:49] Estimating fragment length (mate gap mean=-84.5587, mate gap stddev=29.0902, read length mean=129.466)
[2026-06-03T20:21:49] Filtering read-through fragments with a distance <=10000bp (remaining=5923355)
[2026-06-03T20:21:51] Filtering inconsistently clipped mates (remaining=5803652)
[2026-06-03T20:21:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5631534)
[2026-06-03T20:21:58] Filtering fragments with small insert size (remaining=5630525)
[2026-06-03T20:22:00] Filtering alignments with long gaps (remaining=5630525)
[2026-06-03T20:22:02] Filtering fragments with both mates in the same gene (remaining=5629127)
[2026-06-03T20:22:04] Filtering fusions arising from hairpin structures (remaining=5245572)
[2026-06-03T20:22:07] Filtering reads with a mismatch p-value <=0.01 (remaining=2458012)
[2026-06-03T20:22:20] Filtering reads with low entropy (k-mer content >=60%) (remaining=1224155)
[2026-06-03T20:22:31] Finding fusions and counting supporting reads (total=901407)
[2026-06-03T20:22:48] Merging adjacent fusion breakpoints (remaining=894037)
[2026-06-03T20:22:50] Filtering multi-mapping fusions by alignment score and read support (remaining=567916)
[2026-06-03T20:23:23] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:23:30] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=565748)
[2026-06-03T20:23:31] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=330068)
[2026-06-03T20:23:32] Filtering fusions with <2 supporting reads (remaining=40680)
[2026-06-03T20:23:33] Filtering fusions with an e-value >=0.3 (remaining=10494)
[2026-06-03T20:23:34] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10567)
[2026-06-03T20:23:38] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10413)
[2026-06-03T20:23:38] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10414)
[2026-06-03T20:23:40] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8642)
[2026-06-03T20:23:45] Searching for fusions with spliced split reads (remaining=8668)
[2026-06-03T20:23:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=5183)
[2026-06-03T20:23:52] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5092)
[2026-06-03T20:23:53] Searching for fusions with >=4 spliced events (remaining=6211)
[2026-06-03T20:23:54] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2297)
[2026-06-03T20:24:09] Filtering fusions with anchors <=23nt (remaining=1935)
[2026-06-03T20:24:10] Filtering end-to-end fusions with low support (remaining=1883)
[2026-06-03T20:24:11] Filtering fusions with no coverage around the breakpoints (remaining=1852)
[2026-06-03T20:24:12] Indexing gene sequences 
[2026-06-03T20:24:19] Filtering genes with >=30% identity (remaining=656)
[2026-06-03T20:24:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=348)
[2026-06-03T20:24:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=275)
[2026-06-03T20:24:29] Searching for additional isoforms (remaining=362)
[2026-06-03T20:24:30] Assigning confidence scores to events 
[2026-06-03T20:24:34] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:24:34] Writing fusions to file 'aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:24:38] Writing discarded fusions to file 'aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:25:09] Freeing resources
[2026-06-03T20:25:26] Done (elapsed time=00:11:27, CPU time=00:11:26, peak memory=14.8gb)