[2026-06-03T20:34:42] Launching Arriba 2.4.0
[2026-06-03T20:34:42] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:34:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:34:54] Reading chimeric alignments from 'aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10070930)
[2026-06-03T20:41:21] Marking multi-mapping alignments (marked=6655904)
[2026-06-03T20:41:25] Detecting strandedness (reverse)
[2026-06-03T20:41:25] Assigning strands to alignments 
[2026-06-03T20:41:27] Annotating alignments 
[2026-06-03T20:41:59] Filtering duplicates (remaining=6087690)
[2026-06-03T20:42:06] 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=5674067)
[2026-06-03T20:42:08] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5674067)
[2026-06-03T20:42:09] Filtering viral contigs with expression lower than the top 5 (remaining=5674067)
[2026-06-03T20:42:14] Filtering viral contigs with less than 5% coverage (remaining=5674067)
[2026-06-03T20:42:16] Estimating fragment length (mate gap mean=-85.4846, mate gap stddev=28.246, read length mean=124.884)
[2026-06-03T20:42:16] Filtering read-through fragments with a distance <=10000bp (remaining=5316475)
[2026-06-03T20:42:18] Filtering inconsistently clipped mates (remaining=5181696)
[2026-06-03T20:42:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5033202)
[2026-06-03T20:42:24] Filtering fragments with small insert size (remaining=5031977)
[2026-06-03T20:42:26] Filtering alignments with long gaps (remaining=5031977)
[2026-06-03T20:42:28] Filtering fragments with both mates in the same gene (remaining=5030795)
[2026-06-03T20:42:30] Filtering fusions arising from hairpin structures (remaining=4636423)
[2026-06-03T20:42:33] Filtering reads with a mismatch p-value <=0.01 (remaining=1862544)
[2026-06-03T20:42:45] Filtering reads with low entropy (k-mer content >=60%) (remaining=948427)
[2026-06-03T20:42:54] Finding fusions and counting supporting reads (total=726032)
[2026-06-03T20:43:10] Merging adjacent fusion breakpoints (remaining=718258)
[2026-06-03T20:43:11] Filtering multi-mapping fusions by alignment score and read support (remaining=452436)
[2026-06-03T20:43:42] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:43:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=450772)
[2026-06-03T20:43:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=250207)
[2026-06-03T20:43:50] Filtering fusions with <2 supporting reads (remaining=28605)
[2026-06-03T20:43:51] Filtering fusions with an e-value >=0.3 (remaining=6488)
[2026-06-03T20:43:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6561)
[2026-06-03T20:43:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6456)
[2026-06-03T20:43:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6456)
[2026-06-03T20:43:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6154)
[2026-06-03T20:44:02] Searching for fusions with spliced split reads (remaining=6268)
[2026-06-03T20:44:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=4136)
[2026-06-03T20:44:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4098)
[2026-06-03T20:44:09] Searching for fusions with >=4 spliced events (remaining=4865)
[2026-06-03T20:44:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1902)
[2026-06-03T20:44:25] Filtering fusions with anchors <=23nt (remaining=1486)
[2026-06-03T20:44:26] Filtering end-to-end fusions with low support (remaining=1454)
[2026-06-03T20:44:26] Filtering fusions with no coverage around the breakpoints (remaining=1432)
[2026-06-03T20:44:27] Indexing gene sequences 
[2026-06-03T20:44:33] Filtering genes with >=30% identity (remaining=420)
[2026-06-03T20:44:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=172)
[2026-06-03T20:44:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=170)
[2026-06-03T20:44:39] Searching for additional isoforms (remaining=213)
[2026-06-03T20:44:40] Assigning confidence scores to events 
[2026-06-03T20:44:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:44:44] Writing fusions to file 'aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:44:45] Writing discarded fusions to file 'aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:45:13] Freeing resources
[2026-06-03T20:45:29] Done (elapsed time=00:10:47, CPU time=00:10:46, peak memory=14.9gb)