[2026-06-08T09:04:19] Launching Arriba 2.4.0
[2026-06-08T09:04:19] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:04:28] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:04:32] Reading chimeric alignments from 'aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10959910)
[2026-06-08T09:11:32] Marking multi-mapping alignments (marked=6829752)
[2026-06-08T09:11:37] Detecting strandedness (reverse)
[2026-06-08T09:11:37] Assigning strands to alignments 
[2026-06-08T09:11:40] Annotating alignments 
[2026-06-08T09:12:20] Filtering duplicates (remaining=4531358)
[2026-06-08T09:12:27] 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=4244668)
[2026-06-08T09:12:29] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4244668)
[2026-06-08T09:12:31] Filtering viral contigs with expression lower than the top 5 (remaining=4244668)
[2026-06-08T09:12:36] Filtering viral contigs with less than 5% coverage (remaining=4244668)
[2026-06-08T09:12:39] Estimating fragment length (mate gap mean=-86.5774, mate gap stddev=28.0352, read length mean=126.661)
[2026-06-08T09:12:39] Filtering read-through fragments with a distance <=10000bp (remaining=3980816)
[2026-06-08T09:12:41] Filtering inconsistently clipped mates (remaining=3902725)
[2026-06-08T09:12:44] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3807753)
[2026-06-08T09:12:48] Filtering fragments with small insert size (remaining=3806565)
[2026-06-08T09:12:50] Filtering alignments with long gaps (remaining=3806565)
[2026-06-08T09:12:53] Filtering fragments with both mates in the same gene (remaining=3805790)
[2026-06-08T09:12:55] Filtering fusions arising from hairpin structures (remaining=3583610)
[2026-06-08T09:12:58] Filtering reads with a mismatch p-value <=0.01 (remaining=1469070)
[2026-06-08T09:13:08] Filtering reads with low entropy (k-mer content >=60%) (remaining=623226)
[2026-06-08T09:13:17] Finding fusions and counting supporting reads (total=499800)
[2026-06-08T09:13:34] Merging adjacent fusion breakpoints (remaining=493936)
[2026-06-08T09:13:36] Filtering multi-mapping fusions by alignment score and read support (remaining=307153)
[2026-06-08T09:14:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:14:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=305880)
[2026-06-08T09:14:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=165999)
[2026-06-08T09:14:20] Filtering fusions with <2 supporting reads (remaining=20668)
[2026-06-08T09:14:20] Filtering fusions with an e-value >=0.3 (remaining=4630)
[2026-06-08T09:14:21] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4666)
[2026-06-08T09:14:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4599)
[2026-06-08T09:14:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4599)
[2026-06-08T09:14:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4056)
[2026-06-08T09:14:31] Searching for fusions with spliced split reads (remaining=4140)
[2026-06-08T09:14:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=2977)
[2026-06-08T09:14:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2951)
[2026-06-08T09:14:38] Searching for fusions with >=4 spliced events (remaining=3381)
[2026-06-08T09:14:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1267)
[2026-06-08T09:14:52] Filtering fusions with anchors <=23nt (remaining=1049)
[2026-06-08T09:14:53] Filtering end-to-end fusions with low support (remaining=1006)
[2026-06-08T09:14:53] Filtering fusions with no coverage around the breakpoints (remaining=980)
[2026-06-08T09:14:54] Indexing gene sequences 
[2026-06-08T09:14:59] Filtering genes with >=30% identity (remaining=375)
[2026-06-08T09:15:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=214)
[2026-06-08T09:15:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=188)
[2026-06-08T09:15:04] Searching for additional isoforms (remaining=217)
[2026-06-08T09:15:05] Assigning confidence scores to events 
[2026-06-08T09:15:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:15:08] Writing fusions to file 'aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:15:10] Writing discarded fusions to file 'aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:15:36] Freeing resources
[2026-06-08T09:15:54] Done (elapsed time=00:11:35, CPU time=00:11:34, peak memory=15.6gb)