[2026-06-03T20:30:46] Launching Arriba 2.4.0
[2026-06-03T20:30:46] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:30:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:30:57] Reading chimeric alignments from 'aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=12520196)
[2026-06-03T20:38:25] Marking multi-mapping alignments (marked=8405010)
[2026-06-03T20:38:30] Detecting strandedness (reverse)
[2026-06-03T20:38:30] Assigning strands to alignments 
[2026-06-03T20:38:32] Annotating alignments 
[2026-06-03T20:39:08] Filtering duplicates (remaining=6363015)
[2026-06-03T20:39:16] 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=5688702)
[2026-06-03T20:39:18] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5688702)
[2026-06-03T20:39:21] Filtering viral contigs with expression lower than the top 5 (remaining=5688702)
[2026-06-03T20:39:26] Filtering viral contigs with less than 5% coverage (remaining=5688702)
[2026-06-03T20:39:29] Estimating fragment length (mate gap mean=-83.7258, mate gap stddev=29.3751, read length mean=126.491)
[2026-06-03T20:39:29] Filtering read-through fragments with a distance <=10000bp (remaining=5403027)
[2026-06-03T20:39:31] Filtering inconsistently clipped mates (remaining=5266639)
[2026-06-03T20:39:34] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5134355)
[2026-06-03T20:39:38] Filtering fragments with small insert size (remaining=5132127)
[2026-06-03T20:39:40] Filtering alignments with long gaps (remaining=5132126)
[2026-06-03T20:39:43] Filtering fragments with both mates in the same gene (remaining=5131204)
[2026-06-03T20:39:45] Filtering fusions arising from hairpin structures (remaining=4745946)
[2026-06-03T20:39:48] Filtering reads with a mismatch p-value <=0.01 (remaining=1748372)
[2026-06-03T20:40:00] Filtering reads with low entropy (k-mer content >=60%) (remaining=806239)
[2026-06-03T20:40:10] Finding fusions and counting supporting reads (total=576408)
[2026-06-03T20:40:27] Merging adjacent fusion breakpoints (remaining=568797)
[2026-06-03T20:40:29] Filtering multi-mapping fusions by alignment score and read support (remaining=349684)
[2026-06-03T20:41:04] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:41:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=347601)
[2026-06-03T20:41:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=201670)
[2026-06-03T20:41:11] Filtering fusions with <2 supporting reads (remaining=25014)
[2026-06-03T20:41:12] Filtering fusions with an e-value >=0.3 (remaining=5235)
[2026-06-03T20:41:13] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5348)
[2026-06-03T20:41:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5232)
[2026-06-03T20:41:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5232)
[2026-06-03T20:41:19] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4270)
[2026-06-03T20:41:24] Searching for fusions with spliced split reads (remaining=4343)
[2026-06-03T20:41:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=2652)
[2026-06-03T20:41:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2602)
[2026-06-03T20:41:31] Searching for fusions with >=4 spliced events (remaining=2929)
[2026-06-03T20:41:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1053)
[2026-06-03T20:41:46] Filtering fusions with anchors <=23nt (remaining=773)
[2026-06-03T20:41:47] Filtering end-to-end fusions with low support (remaining=743)
[2026-06-03T20:41:48] Filtering fusions with no coverage around the breakpoints (remaining=728)
[2026-06-03T20:41:48] Indexing gene sequences 
[2026-06-03T20:41:52] Filtering genes with >=30% identity (remaining=282)
[2026-06-03T20:41:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=169)
[2026-06-03T20:41:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=166)
[2026-06-03T20:41:58] Searching for additional isoforms (remaining=187)
[2026-06-03T20:41:59] Assigning confidence scores to events 
[2026-06-03T20:42:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:42:02] Writing fusions to file 'aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:42:03] Writing discarded fusions to file 'aih-tih-sc-eecf9f-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:42:27] Freeing resources
[2026-06-03T20:42:47] Done (elapsed time=00:12:01, CPU time=00:12:00, peak memory=17.3gb)