[2026-06-03T20:23:30] Launching Arriba 2.4.0
[2026-06-03T20:23:30] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:23:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:23:42] Reading chimeric alignments from 'aih-tih-sc-c493d4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=8812899)
[2026-06-03T20:28:58] Marking multi-mapping alignments (marked=5891490)
[2026-06-03T20:29:01] Detecting strandedness (reverse)
[2026-06-03T20:29:01] Assigning strands to alignments 
[2026-06-03T20:29:03] Annotating alignments 
[2026-06-03T20:29:30] Filtering duplicates (remaining=4419395)
[2026-06-03T20:29:34] 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=4067967)
[2026-06-03T20:29:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4067967)
[2026-06-03T20:29:38] Filtering viral contigs with expression lower than the top 5 (remaining=4067967)
[2026-06-03T20:29:41] Filtering viral contigs with less than 5% coverage (remaining=4067967)
[2026-06-03T20:29:43] Estimating fragment length (mate gap mean=-82.8027, mate gap stddev=27.4425, read length mean=118.459)
[2026-06-03T20:29:43] Filtering read-through fragments with a distance <=10000bp (remaining=3838053)
[2026-06-03T20:29:45] Filtering inconsistently clipped mates (remaining=3728991)
[2026-06-03T20:29:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3603750)
[2026-06-03T20:29:50] Filtering fragments with small insert size (remaining=3602177)
[2026-06-03T20:29:52] Filtering alignments with long gaps (remaining=3602177)
[2026-06-03T20:29:54] Filtering fragments with both mates in the same gene (remaining=3601326)
[2026-06-03T20:29:55] Filtering fusions arising from hairpin structures (remaining=3329505)
[2026-06-03T20:29:57] Filtering reads with a mismatch p-value <=0.01 (remaining=1207131)
[2026-06-03T20:30:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=601739)
[2026-06-03T20:30:13] Finding fusions and counting supporting reads (total=473538)
[2026-06-03T20:30:25] Merging adjacent fusion breakpoints (remaining=468112)
[2026-06-03T20:30:26] Filtering multi-mapping fusions by alignment score and read support (remaining=279500)
[2026-06-03T20:30:53] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:30:57] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=278552)
[2026-06-03T20:30:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=158594)
[2026-06-03T20:30:59] Filtering fusions with <2 supporting reads (remaining=17217)
[2026-06-03T20:30:59] Filtering fusions with an e-value >=0.3 (remaining=3491)
[2026-06-03T20:31:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3572)
[2026-06-03T20:31:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3521)
[2026-06-03T20:31:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3521)
[2026-06-03T20:31:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3504)
[2026-06-03T20:31:08] Searching for fusions with spliced split reads (remaining=3560)
[2026-06-03T20:31:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=2578)
[2026-06-03T20:31:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2557)
[2026-06-03T20:31:13] Searching for fusions with >=4 spliced events (remaining=2905)
[2026-06-03T20:31:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1065)
[2026-06-03T20:31:26] Filtering fusions with anchors <=23nt (remaining=894)
[2026-06-03T20:31:27] Filtering end-to-end fusions with low support (remaining=868)
[2026-06-03T20:31:27] Filtering fusions with no coverage around the breakpoints (remaining=855)
[2026-06-03T20:31:28] Indexing gene sequences 
[2026-06-03T20:31:31] Filtering genes with >=30% identity (remaining=264)
[2026-06-03T20:31:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=115)
[2026-06-03T20:31:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=114)
[2026-06-03T20:31:35] Searching for additional isoforms (remaining=134)
[2026-06-03T20:31:36] Assigning confidence scores to events 
[2026-06-03T20:31:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:31:38] Writing fusions to file 'aih-tih-sc-c493d4-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:31:39] Writing discarded fusions to file 'aih-tih-sc-c493d4-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:31:58] Freeing resources
[2026-06-03T20:32:11] Done (elapsed time=00:08:41, CPU time=00:08:40, peak memory=13.4gb)