[2026-06-08T08:49:30] Launching Arriba 2.4.0
[2026-06-08T08:49:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:43] Reading chimeric alignments from 'aih-tih-sc-816ec7-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10637307)
[2026-06-08T08:56:37] Marking multi-mapping alignments (marked=7062138)
[2026-06-08T08:56:42] Detecting strandedness (reverse)
[2026-06-08T08:56:42] Assigning strands to alignments 
[2026-06-08T08:56:44] Annotating alignments 
[2026-06-08T08:57:25] Filtering duplicates (remaining=6960548)
[2026-06-08T08:57:34] 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=6518811)
[2026-06-08T08:57:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6518811)
[2026-06-08T08:57:39] Filtering viral contigs with expression lower than the top 5 (remaining=6518811)
[2026-06-08T08:57:44] Filtering viral contigs with less than 5% coverage (remaining=6518811)
[2026-06-08T08:57:47] Estimating fragment length (mate gap mean=-86.0118, mate gap stddev=29.0746, read length mean=128.808)
[2026-06-08T08:57:47] Filtering read-through fragments with a distance <=10000bp (remaining=6132371)
[2026-06-08T08:57:50] Filtering inconsistently clipped mates (remaining=5994902)
[2026-06-08T08:57:52] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5827514)
[2026-06-08T08:57:58] Filtering fragments with small insert size (remaining=5826518)
[2026-06-08T08:58:00] Filtering alignments with long gaps (remaining=5826518)
[2026-06-08T08:58:03] Filtering fragments with both mates in the same gene (remaining=5825404)
[2026-06-08T08:58:06] Filtering fusions arising from hairpin structures (remaining=5398624)
[2026-06-08T08:58:09] Filtering reads with a mismatch p-value <=0.01 (remaining=2335804)
[2026-06-08T08:58:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=1080138)
[2026-06-08T08:58:36] Finding fusions and counting supporting reads (total=838631)
[2026-06-08T08:58:57] Merging adjacent fusion breakpoints (remaining=829353)
[2026-06-08T08:58:59] Filtering multi-mapping fusions by alignment score and read support (remaining=508633)
[2026-06-08T08:59:37] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:46] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=506546)
[2026-06-08T08:59:47] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=297441)
[2026-06-08T08:59:48] Filtering fusions with <2 supporting reads (remaining=32997)
[2026-06-08T08:59:49] Filtering fusions with an e-value >=0.3 (remaining=8451)
[2026-06-08T08:59:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8500)
[2026-06-08T08:59:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8395)
[2026-06-08T08:59:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8395)
[2026-06-08T08:59:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6955)
[2026-06-08T09:00:03] Searching for fusions with spliced split reads (remaining=7067)
[2026-06-08T09:00:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=4640)
[2026-06-08T09:00:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4585)
[2026-06-08T09:00:11] Searching for fusions with >=4 spliced events (remaining=5442)
[2026-06-08T09:00:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2261)
[2026-06-08T09:00:30] Filtering fusions with anchors <=23nt (remaining=1769)
[2026-06-08T09:00:30] Filtering end-to-end fusions with low support (remaining=1712)
[2026-06-08T09:00:31] Filtering fusions with no coverage around the breakpoints (remaining=1677)
[2026-06-08T09:00:32] Indexing gene sequences 
[2026-06-08T09:00:39] Filtering genes with >=30% identity (remaining=585)
[2026-06-08T09:00:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=257)
[2026-06-08T09:00:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=203)
[2026-06-08T09:00:47] Searching for additional isoforms (remaining=270)
[2026-06-08T09:00:49] Assigning confidence scores to events 
[2026-06-08T09:00:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:54] Writing fusions to file 'aih-tih-sc-816ec7-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:00:56] Writing discarded fusions to file 'aih-tih-sc-816ec7-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:36] Freeing resources
[2026-06-08T09:01:58] Done (elapsed time=00:12:28, CPU time=00:12:27, peak memory=15.4gb)