[2026-06-08T08:35:03] Launching Arriba 2.4.0
[2026-06-08T08:35:03] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:12] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:16] Reading chimeric alignments from 'aih-tih-sc-66e7f5-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=8462547)
[2026-06-08T08:39:53] Marking multi-mapping alignments (marked=5736107)
[2026-06-08T08:39:57] Detecting strandedness (reverse)
[2026-06-08T08:39:57] Assigning strands to alignments 
[2026-06-08T08:39:58] Annotating alignments 
[2026-06-08T08:40:27] Filtering duplicates (remaining=3269105)
[2026-06-08T08:40:31] 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=3012938)
[2026-06-08T08:40:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3012938)
[2026-06-08T08:40:34] Filtering viral contigs with expression lower than the top 5 (remaining=3012938)
[2026-06-08T08:40:38] Filtering viral contigs with less than 5% coverage (remaining=3012938)
[2026-06-08T08:40:40] Estimating fragment length (mate gap mean=-86.5116, mate gap stddev=27.9191, read length mean=125.075)
[2026-06-08T08:40:40] Filtering read-through fragments with a distance <=10000bp (remaining=2875591)
[2026-06-08T08:40:41] Filtering inconsistently clipped mates (remaining=2820135)
[2026-06-08T08:40:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2710424)
[2026-06-08T08:40:46] Filtering fragments with small insert size (remaining=2709761)
[2026-06-08T08:40:47] Filtering alignments with long gaps (remaining=2709761)
[2026-06-08T08:40:49] Filtering fragments with both mates in the same gene (remaining=2709207)
[2026-06-08T08:40:50] Filtering fusions arising from hairpin structures (remaining=2561218)
[2026-06-08T08:40:52] Filtering reads with a mismatch p-value <=0.01 (remaining=1032277)
[2026-06-08T08:41:00] Filtering reads with low entropy (k-mer content >=60%) (remaining=387741)
[2026-06-08T08:41:05] Finding fusions and counting supporting reads (total=335319)
[2026-06-08T08:41:17] Merging adjacent fusion breakpoints (remaining=333216)
[2026-06-08T08:41:18] Filtering multi-mapping fusions by alignment score and read support (remaining=179597)
[2026-06-08T08:41:45] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=178406)
[2026-06-08T08:41:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=104976)
[2026-06-08T08:41:49] Filtering fusions with <2 supporting reads (remaining=11255)
[2026-06-08T08:41:50] Filtering fusions with an e-value >=0.3 (remaining=3146)
[2026-06-08T08:41:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3176)
[2026-06-08T08:41:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3106)
[2026-06-08T08:41:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3106)
[2026-06-08T08:41:54] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2652)
[2026-06-08T08:41:57] Searching for fusions with spliced split reads (remaining=2698)
[2026-06-08T08:42:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=2003)
[2026-06-08T08:42:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1969)
[2026-06-08T08:42:02] Searching for fusions with >=4 spliced events (remaining=2122)
[2026-06-08T08:42:02] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=718)
[2026-06-08T08:42:14] Filtering fusions with anchors <=23nt (remaining=578)
[2026-06-08T08:42:14] Filtering end-to-end fusions with low support (remaining=551)
[2026-06-08T08:42:15] Filtering fusions with no coverage around the breakpoints (remaining=534)
[2026-06-08T08:42:15] Indexing gene sequences 
[2026-06-08T08:42:18] Filtering genes with >=30% identity (remaining=192)
[2026-06-08T08:42:19] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=102)
[2026-06-08T08:42:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=102)
[2026-06-08T08:42:21] Searching for additional isoforms (remaining=112)
[2026-06-08T08:42:22] Assigning confidence scores to events 
[2026-06-08T08:42:24] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:42:24] Writing fusions to file 'aih-tih-sc-66e7f5-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:42:24] Writing discarded fusions to file 'aih-tih-sc-66e7f5-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:41] Freeing resources
[2026-06-08T08:42:53] Done (elapsed time=00:07:50, CPU time=00:07:49, peak memory=12.9gb)