[2026-06-03T20:14:59] Launching Arriba 2.4.0
[2026-06-03T20:14:59] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:15:08] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:15:12] Reading chimeric alignments from 'aih-tih-sc-714733-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10429951)
[2026-06-03T20:21:58] Marking multi-mapping alignments (marked=6687794)
[2026-06-03T20:22:02] Detecting strandedness (reverse)
[2026-06-03T20:22:02] Assigning strands to alignments 
[2026-06-03T20:22:04] Annotating alignments 
[2026-06-03T20:22:40] Filtering duplicates (remaining=6731654)
[2026-06-03T20:22:48] 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=6327193)
[2026-06-03T20:22:50] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6327193)
[2026-06-03T20:22:52] Filtering viral contigs with expression lower than the top 5 (remaining=6327193)
[2026-06-03T20:22:57] Filtering viral contigs with less than 5% coverage (remaining=6327193)
[2026-06-03T20:22:59] Estimating fragment length (mate gap mean=-85.6513, mate gap stddev=29.6961, read length mean=130.653)
[2026-06-03T20:22:59] Filtering read-through fragments with a distance <=10000bp (remaining=5929988)
[2026-06-03T20:23:01] Filtering inconsistently clipped mates (remaining=5804761)
[2026-06-03T20:23:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5638744)
[2026-06-03T20:23:08] Filtering fragments with small insert size (remaining=5637680)
[2026-06-03T20:23:10] Filtering alignments with long gaps (remaining=5637680)
[2026-06-03T20:23:12] Filtering fragments with both mates in the same gene (remaining=5636702)
[2026-06-03T20:23:14] Filtering fusions arising from hairpin structures (remaining=5233262)
[2026-06-03T20:23:17] Filtering reads with a mismatch p-value <=0.01 (remaining=2394157)
[2026-06-03T20:23:31] Filtering reads with low entropy (k-mer content >=60%) (remaining=1204117)
[2026-06-03T20:23:42] Finding fusions and counting supporting reads (total=864615)
[2026-06-03T20:23:58] Merging adjacent fusion breakpoints (remaining=857414)
[2026-06-03T20:24:00] Filtering multi-mapping fusions by alignment score and read support (remaining=544137)
[2026-06-03T20:24:32] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:24:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=541402)
[2026-06-03T20:24:40] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=320400)
[2026-06-03T20:24:41] Filtering fusions with <2 supporting reads (remaining=47191)
[2026-06-03T20:24:42] Filtering fusions with an e-value >=0.3 (remaining=14530)
[2026-06-03T20:24:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14583)
[2026-06-03T20:24:47] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14466)
[2026-06-03T20:24:47] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14466)
[2026-06-03T20:24:49] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9290)
[2026-06-03T20:24:54] Searching for fusions with spliced split reads (remaining=9323)
[2026-06-03T20:24:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=5678)
[2026-06-03T20:25:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5616)
[2026-06-03T20:25:01] Searching for fusions with >=4 spliced events (remaining=7170)
[2026-06-03T20:25:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3147)
[2026-06-03T20:25:19] Filtering fusions with anchors <=23nt (remaining=2694)
[2026-06-03T20:25:19] Filtering end-to-end fusions with low support (remaining=2617)
[2026-06-03T20:25:20] Filtering fusions with no coverage around the breakpoints (remaining=2569)
[2026-06-03T20:25:21] Indexing gene sequences 
[2026-06-03T20:25:31] Filtering genes with >=30% identity (remaining=1145)
[2026-06-03T20:25:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=800)
[2026-06-03T20:26:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=474)
[2026-06-03T20:26:04] Searching for additional isoforms (remaining=716)
[2026-06-03T20:26:06] Assigning confidence scores to events 
[2026-06-03T20:26:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:26:09] Writing fusions to file 'aih-tih-sc-714733-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:26:16] Writing discarded fusions to file 'aih-tih-sc-714733-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:26:46] Freeing resources
[2026-06-03T20:27:03] Done (elapsed time=00:12:04, CPU time=00:12:03, peak memory=15.5gb)