[2026-06-03T22:36:32] Launching Arriba 2.4.0
[2026-06-03T22:36:32] Loading assembly from 'ref_genome.fa' 
[2026-06-03T22:36:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T22:36:43] Reading chimeric alignments from 'aih-tih-sc-f7ac14-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=12904803)
[2026-06-03T22:43:57] Marking multi-mapping alignments (marked=9209901)
[2026-06-03T22:44:03] Detecting strandedness (reverse)
[2026-06-03T22:44:03] Assigning strands to alignments 
[2026-06-03T22:44:06] Annotating alignments 
[2026-06-03T22:44:58] Filtering duplicates (remaining=4834519)
[2026-06-03T22:45:06] 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=4325599)
[2026-06-03T22:45:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4325599)
[2026-06-03T22:45:13] Filtering viral contigs with expression lower than the top 5 (remaining=4325599)
[2026-06-03T22:45:20] Filtering viral contigs with less than 5% coverage (remaining=4325599)
[2026-06-03T22:45:24] Estimating fragment length (mate gap mean=-78.3256, mate gap stddev=28.4023, read length mean=112.699)
[2026-06-03T22:45:24] Filtering read-through fragments with a distance <=10000bp (remaining=4104925)
[2026-06-03T22:45:28] Filtering inconsistently clipped mates (remaining=3995804)
[2026-06-03T22:45:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3833142)
[2026-06-03T22:45:37] Filtering fragments with small insert size (remaining=3831605)
[2026-06-03T22:45:40] Filtering alignments with long gaps (remaining=3831605)
[2026-06-03T22:45:43] Filtering fragments with both mates in the same gene (remaining=3830438)
[2026-06-03T22:45:47] Filtering fusions arising from hairpin structures (remaining=3598388)
[2026-06-03T22:45:51] Filtering reads with a mismatch p-value <=0.01 (remaining=1210859)
[2026-06-03T22:46:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=507174)
[2026-06-03T22:46:13] Finding fusions and counting supporting reads (total=438433)
[2026-06-03T22:46:37] Merging adjacent fusion breakpoints (remaining=434058)
[2026-06-03T22:46:39] Filtering multi-mapping fusions by alignment score and read support (remaining=245836)
[2026-06-03T22:47:22] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T22:47:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=244628)
[2026-06-03T22:47:29] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=143613)
[2026-06-03T22:47:30] Filtering fusions with <2 supporting reads (remaining=13104)
[2026-06-03T22:47:31] Filtering fusions with an e-value >=0.3 (remaining=2747)
[2026-06-03T22:47:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2781)
[2026-06-03T22:47:36] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2716)
[2026-06-03T22:47:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2716)
[2026-06-03T22:47:38] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2655)
[2026-06-03T22:47:44] Searching for fusions with spliced split reads (remaining=2716)
[2026-06-03T22:47:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=2014)
[2026-06-03T22:47:51] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1996)
[2026-06-03T22:47:51] Searching for fusions with >=4 spliced events (remaining=2244)
[2026-06-03T22:47:53] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=904)
[2026-06-03T22:48:07] Filtering fusions with anchors <=23nt (remaining=712)
[2026-06-03T22:48:08] Filtering end-to-end fusions with low support (remaining=687)
[2026-06-03T22:48:08] Filtering fusions with no coverage around the breakpoints (remaining=677)
[2026-06-03T22:48:09] Indexing gene sequences 
[2026-06-03T22:48:12] Filtering genes with >=30% identity (remaining=230)
[2026-06-03T22:48:14] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=101)
[2026-06-03T22:48:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=86)
[2026-06-03T22:48:17] Searching for additional isoforms (remaining=102)
[2026-06-03T22:48:18] Assigning confidence scores to events 
[2026-06-03T22:48:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T22:48:21] Writing fusions to file 'aih-tih-sc-f7ac14-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T22:48:22] Writing discarded fusions to file 'aih-tih-sc-f7ac14-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T22:48:50] Freeing resources
[2026-06-03T22:49:09] Done (elapsed time=00:12:37, CPU time=00:12:36, peak memory=17.4gb)