[2026-06-08T08:39:13] Launching Arriba 2.4.0
[2026-06-08T08:39:13] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:28] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:32] Reading chimeric alignments from 'aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10546818)
[2026-06-08T08:46:54] Marking multi-mapping alignments (marked=7200642)
[2026-06-08T08:46:59] Detecting strandedness (reverse)
[2026-06-08T08:46:59] Assigning strands to alignments 
[2026-06-08T08:47:01] Annotating alignments 
[2026-06-08T08:47:33] Filtering duplicates (remaining=4082868)
[2026-06-08T08:47:39] 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=3789611)
[2026-06-08T08:47:41] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3789611)
[2026-06-08T08:47:43] Filtering viral contigs with expression lower than the top 5 (remaining=3789611)
[2026-06-08T08:47:47] Filtering viral contigs with less than 5% coverage (remaining=3789611)
[2026-06-08T08:47:50] Estimating fragment length (mate gap mean=-84.8162, mate gap stddev=28.8996, read length mean=127.899)
[2026-06-08T08:47:50] Filtering read-through fragments with a distance <=10000bp (remaining=3631180)
[2026-06-08T08:47:52] Filtering inconsistently clipped mates (remaining=3561941)
[2026-06-08T08:47:54] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3426053)
[2026-06-08T08:47:58] Filtering fragments with small insert size (remaining=3425393)
[2026-06-08T08:48:00] Filtering alignments with long gaps (remaining=3425392)
[2026-06-08T08:48:02] Filtering fragments with both mates in the same gene (remaining=3424659)
[2026-06-08T08:48:04] Filtering fusions arising from hairpin structures (remaining=3236317)
[2026-06-08T08:48:06] Filtering reads with a mismatch p-value <=0.01 (remaining=1416350)
[2026-06-08T08:48:16] Filtering reads with low entropy (k-mer content >=60%) (remaining=460469)
[2026-06-08T08:48:24] Finding fusions and counting supporting reads (total=378691)
[2026-06-08T08:48:39] Merging adjacent fusion breakpoints (remaining=375913)
[2026-06-08T08:48:40] Filtering multi-mapping fusions by alignment score and read support (remaining=208064)
[2026-06-08T08:49:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=206834)
[2026-06-08T08:49:16] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=121328)
[2026-06-08T08:49:17] Filtering fusions with <2 supporting reads (remaining=13001)
[2026-06-08T08:49:18] Filtering fusions with an e-value >=0.3 (remaining=3527)
[2026-06-08T08:49:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3555)
[2026-06-08T08:49:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3468)
[2026-06-08T08:49:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3469)
[2026-06-08T08:49:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3126)
[2026-06-08T08:49:27] Searching for fusions with spliced split reads (remaining=3206)
[2026-06-08T08:49:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=2324)
[2026-06-08T08:49:32] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2300)
[2026-06-08T08:49:32] Searching for fusions with >=4 spliced events (remaining=2596)
[2026-06-08T08:49:33] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=864)
[2026-06-08T08:49:49] Filtering fusions with anchors <=23nt (remaining=691)
[2026-06-08T08:49:49] Filtering end-to-end fusions with low support (remaining=667)
[2026-06-08T08:49:49] Filtering fusions with no coverage around the breakpoints (remaining=646)
[2026-06-08T08:49:50] Indexing gene sequences 
[2026-06-08T08:49:54] Filtering genes with >=30% identity (remaining=211)
[2026-06-08T08:49:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=102)
[2026-06-08T08:50:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=87)
[2026-06-08T08:50:01] Searching for additional isoforms (remaining=122)
[2026-06-08T08:50:01] Assigning confidence scores to events 
[2026-06-08T08:50:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:50:04] Writing fusions to file 'aih-tih-sc-06a169-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:50:05] Writing discarded fusions to file 'aih-tih-sc-06a169-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:25] Freeing resources
[2026-06-08T08:50:41] Done (elapsed time=00:11:28, CPU time=00:11:27, peak memory=14.9gb)