[2026-06-03T20:13:14] Launching Arriba 2.4.0
[2026-06-03T20:13:14] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:13:22] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:13:26] Reading chimeric alignments from 'aih-tih-sc-7f9674-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9469775)
[2026-06-03T20:20:18] Marking multi-mapping alignments (marked=5946385)
[2026-06-03T20:20:23] Detecting strandedness (reverse)
[2026-06-03T20:20:23] Assigning strands to alignments 
[2026-06-03T20:20:25] Annotating alignments 
[2026-06-03T20:21:02] Filtering duplicates (remaining=6434574)
[2026-06-03T20:21:10] 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=6083080)
[2026-06-03T20:21:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6083080)
[2026-06-03T20:21:15] Filtering viral contigs with expression lower than the top 5 (remaining=6083080)
[2026-06-03T20:21:20] Filtering viral contigs with less than 5% coverage (remaining=6083080)
[2026-06-03T20:21:22] Estimating fragment length (mate gap mean=-84.137, mate gap stddev=29.4082, read length mean=128.02)
[2026-06-03T20:21:22] Filtering read-through fragments with a distance <=10000bp (remaining=5692723)
[2026-06-03T20:21:24] Filtering inconsistently clipped mates (remaining=5569006)
[2026-06-03T20:21:27] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5418495)
[2026-06-03T20:21:32] Filtering fragments with small insert size (remaining=5417334)
[2026-06-03T20:21:34] Filtering alignments with long gaps (remaining=5417334)
[2026-06-03T20:21:36] Filtering fragments with both mates in the same gene (remaining=5416010)
[2026-06-03T20:21:39] Filtering fusions arising from hairpin structures (remaining=5016380)
[2026-06-03T20:21:42] Filtering reads with a mismatch p-value <=0.01 (remaining=2268718)
[2026-06-03T20:21:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=1153531)
[2026-06-03T20:22:08] Finding fusions and counting supporting reads (total=866742)
[2026-06-03T20:22:27] Merging adjacent fusion breakpoints (remaining=857980)
[2026-06-03T20:22:28] Filtering multi-mapping fusions by alignment score and read support (remaining=571876)
[2026-06-03T20:23:03] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:23:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=569743)
[2026-06-03T20:23:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=338392)
[2026-06-03T20:23:13] Filtering fusions with <2 supporting reads (remaining=37795)
[2026-06-03T20:23:14] Filtering fusions with an e-value >=0.3 (remaining=9667)
[2026-06-03T20:23:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9735)
[2026-06-03T20:23:18] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9656)
[2026-06-03T20:23:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9656)
[2026-06-03T20:23:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7988)
[2026-06-03T20:23:26] Searching for fusions with spliced split reads (remaining=8006)
[2026-06-03T20:23:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=4884)
[2026-06-03T20:23:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4829)
[2026-06-03T20:23:34] Searching for fusions with >=4 spliced events (remaining=5814)
[2026-06-03T20:23:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1914)
[2026-06-03T20:23:51] Filtering fusions with anchors <=23nt (remaining=1595)
[2026-06-03T20:23:52] Filtering end-to-end fusions with low support (remaining=1550)
[2026-06-03T20:23:53] Filtering fusions with no coverage around the breakpoints (remaining=1518)
[2026-06-03T20:23:54] Indexing gene sequences 
[2026-06-03T20:23:59] Filtering genes with >=30% identity (remaining=445)
[2026-06-03T20:24:02] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=207)
[2026-06-03T20:24:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=204)
[2026-06-03T20:24:10] Searching for additional isoforms (remaining=233)
[2026-06-03T20:24:11] Assigning confidence scores to events 
[2026-06-03T20:24:15] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:24:15] Writing fusions to file 'aih-tih-sc-7f9674-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:24:17] Writing discarded fusions to file 'aih-tih-sc-7f9674-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:24:53] Freeing resources
[2026-06-03T20:25:10] Done (elapsed time=00:11:56, CPU time=00:11:55, peak memory=14.2gb)