[2026-06-03T20:14:50] Launching Arriba 2.4.0
[2026-06-03T20:14:50] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:14:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:15:03] Reading chimeric alignments from 'aih-tih-sc-a8a787-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9915987)
[2026-06-03T20:22:09] Marking multi-mapping alignments (marked=6389492)
[2026-06-03T20:22:13] Detecting strandedness (reverse)
[2026-06-03T20:22:13] Assigning strands to alignments 
[2026-06-03T20:22:15] Annotating alignments 
[2026-06-03T20:22:53] Filtering duplicates (remaining=7188036)
[2026-06-03T20:23:02] 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=6664774)
[2026-06-03T20:23:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6664774)
[2026-06-03T20:23:06] Filtering viral contigs with expression lower than the top 5 (remaining=6664774)
[2026-06-03T20:23:11] Filtering viral contigs with less than 5% coverage (remaining=6664774)
[2026-06-03T20:23:14] Estimating fragment length (mate gap mean=-85.6962, mate gap stddev=31.6061, read length mean=134.323)
[2026-06-03T20:23:14] Filtering read-through fragments with a distance <=10000bp (remaining=6334193)
[2026-06-03T20:23:16] Filtering inconsistently clipped mates (remaining=6231183)
[2026-06-03T20:23:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6064792)
[2026-06-03T20:23:25] Filtering fragments with small insert size (remaining=6064025)
[2026-06-03T20:23:27] Filtering alignments with long gaps (remaining=6064023)
[2026-06-03T20:23:29] Filtering fragments with both mates in the same gene (remaining=6062844)
[2026-06-03T20:23:32] Filtering fusions arising from hairpin structures (remaining=5667809)
[2026-06-03T20:23:35] Filtering reads with a mismatch p-value <=0.01 (remaining=2548063)
[2026-06-03T20:23:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=1186508)
[2026-06-03T20:24:04] Finding fusions and counting supporting reads (total=927300)
[2026-06-03T20:24:25] Merging adjacent fusion breakpoints (remaining=919006)
[2026-06-03T20:24:27] Filtering multi-mapping fusions by alignment score and read support (remaining=611561)
[2026-06-03T20:25:04] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:25:13] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=608842)
[2026-06-03T20:25:14] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=380588)
[2026-06-03T20:25:15] Filtering fusions with <2 supporting reads (remaining=51655)
[2026-06-03T20:25:16] Filtering fusions with an e-value >=0.3 (remaining=23450)
[2026-06-03T20:25:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=23513)
[2026-06-03T20:25:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=23417)
[2026-06-03T20:25:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=23417)
[2026-06-03T20:25:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8690)
[2026-06-03T20:25:30] Searching for fusions with spliced split reads (remaining=8727)
[2026-06-03T20:25:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=4347)
[2026-06-03T20:25:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4304)
[2026-06-03T20:25:39] Searching for fusions with >=4 spliced events (remaining=5392)
[2026-06-03T20:25:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2159)
[2026-06-03T20:25:56] Filtering fusions with anchors <=23nt (remaining=1657)
[2026-06-03T20:25:57] Filtering end-to-end fusions with low support (remaining=1591)
[2026-06-03T20:25:58] Filtering fusions with no coverage around the breakpoints (remaining=1553)
[2026-06-03T20:25:58] Indexing gene sequences 
[2026-06-03T20:26:05] Filtering genes with >=30% identity (remaining=504)
[2026-06-03T20:26:09] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=261)
[2026-06-03T20:26:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=199)
[2026-06-03T20:26:17] Searching for additional isoforms (remaining=274)
[2026-06-03T20:26:18] Assigning confidence scores to events 
[2026-06-03T20:26:22] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:26:22] Writing fusions to file 'aih-tih-sc-a8a787-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:26:25] Writing discarded fusions to file 'aih-tih-sc-a8a787-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:27:04] Freeing resources
[2026-06-03T20:27:22] Done (elapsed time=00:12:32, CPU time=00:12:30, peak memory=14.9gb)