[2026-06-03T20:04:28] Launching Arriba 2.4.0
[2026-06-03T20:04:28] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:04:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:04:51] Reading chimeric alignments from 'aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9196568)
[2026-06-03T20:12:14] Marking multi-mapping alignments (marked=6314464)
[2026-06-03T20:12:18] Detecting strandedness (reverse)
[2026-06-03T20:12:18] Assigning strands to alignments 
[2026-06-03T20:12:20] Annotating alignments 
[2026-06-03T20:12:50] Filtering duplicates (remaining=4349815)
[2026-06-03T20:12:56] 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=3958317)
[2026-06-03T20:12:57] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3958317)
[2026-06-03T20:12:59] Filtering viral contigs with expression lower than the top 5 (remaining=3958317)
[2026-06-03T20:13:03] Filtering viral contigs with less than 5% coverage (remaining=3958317)
[2026-06-03T20:13:05] Estimating fragment length (mate gap mean=-86.0052, mate gap stddev=28.1343, read length mean=124.523)
[2026-06-03T20:13:05] Filtering read-through fragments with a distance <=10000bp (remaining=3769127)
[2026-06-03T20:13:07] Filtering inconsistently clipped mates (remaining=3665681)
[2026-06-03T20:13:09] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3526348)
[2026-06-03T20:13:12] Filtering fragments with small insert size (remaining=3525360)
[2026-06-03T20:13:14] Filtering alignments with long gaps (remaining=3525360)
[2026-06-03T20:13:16] Filtering fragments with both mates in the same gene (remaining=3524506)
[2026-06-03T20:13:18] Filtering fusions arising from hairpin structures (remaining=3242020)
[2026-06-03T20:13:20] Filtering reads with a mismatch p-value <=0.01 (remaining=1256801)
[2026-06-03T20:13:28] Filtering reads with low entropy (k-mer content >=60%) (remaining=546065)
[2026-06-03T20:13:36] Finding fusions and counting supporting reads (total=446019)
[2026-06-03T20:13:50] Merging adjacent fusion breakpoints (remaining=441493)
[2026-06-03T20:13:51] Filtering multi-mapping fusions by alignment score and read support (remaining=253685)
[2026-06-03T20:14:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:14:25] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=251896)
[2026-06-03T20:14:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=146444)
[2026-06-03T20:14:26] Filtering fusions with <2 supporting reads (remaining=15998)
[2026-06-03T20:14:26] Filtering fusions with an e-value >=0.3 (remaining=4554)
[2026-06-03T20:14:27] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4612)
[2026-06-03T20:14:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4535)
[2026-06-03T20:14:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4535)
[2026-06-03T20:14:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3621)
[2026-06-03T20:14:36] Searching for fusions with spliced split reads (remaining=3690)
[2026-06-03T20:14:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=2593)
[2026-06-03T20:14:41] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2551)
[2026-06-03T20:14:41] Searching for fusions with >=4 spliced events (remaining=2857)
[2026-06-03T20:14:42] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1014)
[2026-06-03T20:15:00] Filtering fusions with anchors <=23nt (remaining=835)
[2026-06-03T20:15:00] Filtering end-to-end fusions with low support (remaining=821)
[2026-06-03T20:15:01] Filtering fusions with no coverage around the breakpoints (remaining=803)
[2026-06-03T20:15:01] Indexing gene sequences 
[2026-06-03T20:15:07] Filtering genes with >=30% identity (remaining=326)
[2026-06-03T20:15:09] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=228)
[2026-06-03T20:15:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=185)
[2026-06-03T20:15:12] Searching for additional isoforms (remaining=211)
[2026-06-03T20:15:13] Assigning confidence scores to events 
[2026-06-03T20:15:16] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:15:16] Writing fusions to file 'aih-tih-sc-45523c-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:15:17] Writing discarded fusions to file 'aih-tih-sc-45523c-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:15:41] Freeing resources
[2026-06-03T20:15:57] Done (elapsed time=00:11:29, CPU time=00:11:27, peak memory=13.9gb)