[2026-06-08T08:13:47] Launching Arriba 2.4.0
[2026-06-08T08:13:47] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:14:01] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:14:06] Reading chimeric alignments from 'aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=8061105)
[2026-06-08T08:19:03] Marking multi-mapping alignments (marked=5260079)
[2026-06-08T08:19:07] Detecting strandedness (reverse)
[2026-06-08T08:19:07] Assigning strands to alignments 
[2026-06-08T08:19:08] Annotating alignments 
[2026-06-08T08:19:32] Filtering duplicates (remaining=3131173)
[2026-06-08T08:19:36] 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=2958564)
[2026-06-08T08:19:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2958564)
[2026-06-08T08:19:39] Filtering viral contigs with expression lower than the top 5 (remaining=2958564)
[2026-06-08T08:19:42] Filtering viral contigs with less than 5% coverage (remaining=2958564)
[2026-06-08T08:19:44] Estimating fragment length (mate gap mean=-83.2711, mate gap stddev=27.2477, read length mean=121.489)
[2026-06-08T08:19:44] Filtering read-through fragments with a distance <=10000bp (remaining=2813405)
[2026-06-08T08:19:46] Filtering inconsistently clipped mates (remaining=2765778)
[2026-06-08T08:19:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2663744)
[2026-06-08T08:19:49] Filtering fragments with small insert size (remaining=2663211)
[2026-06-08T08:19:51] Filtering alignments with long gaps (remaining=2663211)
[2026-06-08T08:19:52] Filtering fragments with both mates in the same gene (remaining=2662346)
[2026-06-08T08:19:54] Filtering fusions arising from hairpin structures (remaining=2561719)
[2026-06-08T08:19:55] Filtering reads with a mismatch p-value <=0.01 (remaining=1054787)
[2026-06-08T08:20:02] Filtering reads with low entropy (k-mer content >=60%) (remaining=339929)
[2026-06-08T08:20:07] Finding fusions and counting supporting reads (total=288262)
[2026-06-08T08:20:17] Merging adjacent fusion breakpoints (remaining=284735)
[2026-06-08T08:20:18] Filtering multi-mapping fusions by alignment score and read support (remaining=159167)
[2026-06-08T08:20:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:20:44] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=158431)
[2026-06-08T08:20:44] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=96357)
[2026-06-08T08:20:45] Filtering fusions with <2 supporting reads (remaining=11405)
[2026-06-08T08:20:45] Filtering fusions with an e-value >=0.3 (remaining=2758)
[2026-06-08T08:20:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2790)
[2026-06-08T08:20:48] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2739)
[2026-06-08T08:20:48] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2739)
[2026-06-08T08:20:49] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2719)
[2026-06-08T08:20:52] Searching for fusions with spliced split reads (remaining=2851)
[2026-06-08T08:20:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=2050)
[2026-06-08T08:20:56] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2012)
[2026-06-08T08:20:56] Searching for fusions with >=4 spliced events (remaining=2239)
[2026-06-08T08:20:57] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=665)
[2026-06-08T08:21:12] Filtering fusions with anchors <=23nt (remaining=562)
[2026-06-08T08:21:13] Filtering end-to-end fusions with low support (remaining=551)
[2026-06-08T08:21:13] Filtering fusions with no coverage around the breakpoints (remaining=543)
[2026-06-08T08:21:13] Indexing gene sequences 
[2026-06-08T08:21:17] Filtering genes with >=30% identity (remaining=210)
[2026-06-08T08:21:18] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=116)
[2026-06-08T08:21:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=116)
[2026-06-08T08:21:20] Searching for additional isoforms (remaining=128)
[2026-06-08T08:21:20] Assigning confidence scores to events 
[2026-06-08T08:21:22] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:21:22] Writing fusions to file 'aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:21:23] Writing discarded fusions to file 'aih-tih-sc-18a6f2-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:21:39] Freeing resources
[2026-06-08T08:21:51] Done (elapsed time=00:08:04, CPU time=00:08:03, peak memory=12.2gb)