[2026-06-03T20:54:41] Launching Arriba 2.4.0
[2026-06-03T20:54:41] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:54:49] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:54:53] Reading chimeric alignments from 'aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9722572)
[2026-06-03T21:01:25] Marking multi-mapping alignments (marked=6253568)
[2026-06-03T21:01:29] Detecting strandedness (reverse)
[2026-06-03T21:01:29] Assigning strands to alignments 
[2026-06-03T21:01:31] Annotating alignments 
[2026-06-03T21:02:03] Filtering duplicates (remaining=6943727)
[2026-06-03T21:02:10] 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=6596321)
[2026-06-03T21:02:12] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6596321)
[2026-06-03T21:02:14] Filtering viral contigs with expression lower than the top 5 (remaining=6596321)
[2026-06-03T21:02:19] Filtering viral contigs with less than 5% coverage (remaining=6596321)
[2026-06-03T21:02:21] Estimating fragment length (mate gap mean=-85.9368, mate gap stddev=29.1834, read length mean=130.955)
[2026-06-03T21:02:21] Filtering read-through fragments with a distance <=10000bp (remaining=6197067)
[2026-06-03T21:02:23] Filtering inconsistently clipped mates (remaining=6060990)
[2026-06-03T21:02:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5884023)
[2026-06-03T21:02:30] Filtering fragments with small insert size (remaining=5883241)
[2026-06-03T21:02:31] Filtering alignments with long gaps (remaining=5883241)
[2026-06-03T21:02:33] Filtering fragments with both mates in the same gene (remaining=5882070)
[2026-06-03T21:02:36] Filtering fusions arising from hairpin structures (remaining=5455897)
[2026-06-03T21:02:38] Filtering reads with a mismatch p-value <=0.01 (remaining=2514743)
[2026-06-03T21:02:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=1289069)
[2026-06-03T21:03:05] Finding fusions and counting supporting reads (total=1016073)
[2026-06-03T21:03:22] Merging adjacent fusion breakpoints (remaining=1008224)
[2026-06-03T21:03:24] Filtering multi-mapping fusions by alignment score and read support (remaining=640363)
[2026-06-03T21:03:57] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T21:04:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=638630)
[2026-06-03T21:04:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=403200)
[2026-06-03T21:04:07] Filtering fusions with <2 supporting reads (remaining=35343)
[2026-06-03T21:04:08] Filtering fusions with an e-value >=0.3 (remaining=8249)
[2026-06-03T21:04:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8316)
[2026-06-03T21:04:13] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8213)
[2026-06-03T21:04:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8213)
[2026-06-03T21:04:15] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6935)
[2026-06-03T21:04:20] Searching for fusions with spliced split reads (remaining=6981)
[2026-06-03T21:04:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=4390)
[2026-06-03T21:04:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4344)
[2026-06-03T21:04:28] Searching for fusions with >=4 spliced events (remaining=5580)
[2026-06-03T21:04:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2724)
[2026-06-03T21:04:45] Filtering fusions with anchors <=23nt (remaining=2308)
[2026-06-03T21:04:45] Filtering end-to-end fusions with low support (remaining=2248)
[2026-06-03T21:04:46] Filtering fusions with no coverage around the breakpoints (remaining=2207)
[2026-06-03T21:04:47] Indexing gene sequences 
[2026-06-03T21:04:55] Filtering genes with >=30% identity (remaining=838)
[2026-06-03T21:05:06] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=529)
[2026-06-03T21:05:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=324)
[2026-06-03T21:05:17] Searching for additional isoforms (remaining=456)
[2026-06-03T21:05:19] Assigning confidence scores to events 
[2026-06-03T21:05:23] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T21:05:23] Writing fusions to file 'aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T21:05:27] Writing discarded fusions to file 'aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T21:06:00] Freeing resources
[2026-06-03T21:06:16] Done (elapsed time=00:11:35, CPU time=00:11:34, peak memory=14.6gb)