[2026-06-03T20:10:51] Launching Arriba 2.4.0
[2026-06-03T20:10:51] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:11:00] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:11:04] Reading chimeric alignments from 'aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11115020)
[2026-06-03T20:18:41] Marking multi-mapping alignments (marked=7576376)
[2026-06-03T20:18:46] Detecting strandedness (reverse)
[2026-06-03T20:18:46] Assigning strands to alignments 
[2026-06-03T20:18:49] Annotating alignments 
[2026-06-03T20:19:29] Filtering duplicates (remaining=6897245)
[2026-06-03T20:19:38] 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=6360130)
[2026-06-03T20:19:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6360130)
[2026-06-03T20:19:42] Filtering viral contigs with expression lower than the top 5 (remaining=6360130)
[2026-06-03T20:19:47] Filtering viral contigs with less than 5% coverage (remaining=6360130)
[2026-06-03T20:19:50] Estimating fragment length (mate gap mean=-86.6113, mate gap stddev=28.639, read length mean=126.174)
[2026-06-03T20:19:50] Filtering read-through fragments with a distance <=10000bp (remaining=6021583)
[2026-06-03T20:19:53] Filtering inconsistently clipped mates (remaining=5897769)
[2026-06-03T20:19:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5747347)
[2026-06-03T20:20:00] Filtering fragments with small insert size (remaining=5746272)
[2026-06-03T20:20:02] Filtering alignments with long gaps (remaining=5746272)
[2026-06-03T20:20:05] Filtering fragments with both mates in the same gene (remaining=5745172)
[2026-06-03T20:20:07] Filtering fusions arising from hairpin structures (remaining=5372746)
[2026-06-03T20:20:10] Filtering reads with a mismatch p-value <=0.01 (remaining=2091663)
[2026-06-03T20:20:25] Filtering reads with low entropy (k-mer content >=60%) (remaining=959258)
[2026-06-03T20:20:36] Finding fusions and counting supporting reads (total=755938)
[2026-06-03T20:20:57] Merging adjacent fusion breakpoints (remaining=748590)
[2026-06-03T20:20:59] Filtering multi-mapping fusions by alignment score and read support (remaining=461805)
[2026-06-03T20:21:37] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:21:45] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=459846)
[2026-06-03T20:21:46] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=276980)
[2026-06-03T20:21:47] Filtering fusions with <2 supporting reads (remaining=32118)
[2026-06-03T20:21:48] Filtering fusions with an e-value >=0.3 (remaining=8911)
[2026-06-03T20:21:49] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8974)
[2026-06-03T20:21:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8905)
[2026-06-03T20:21:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8905)
[2026-06-03T20:21:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6195)
[2026-06-03T20:22:01] Searching for fusions with spliced split reads (remaining=6219)
[2026-06-03T20:22:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=4120)
[2026-06-03T20:22:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4059)
[2026-06-03T20:22:09] Searching for fusions with >=4 spliced events (remaining=4910)
[2026-06-03T20:22:11] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1998)
[2026-06-03T20:22:25] Filtering fusions with anchors <=23nt (remaining=1545)
[2026-06-03T20:22:26] Filtering end-to-end fusions with low support (remaining=1493)
[2026-06-03T20:22:26] Filtering fusions with no coverage around the breakpoints (remaining=1468)
[2026-06-03T20:22:27] Indexing gene sequences 
[2026-06-03T20:22:34] Filtering genes with >=30% identity (remaining=464)
[2026-06-03T20:22:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=246)
[2026-06-03T20:22:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=216)
[2026-06-03T20:22:46] Searching for additional isoforms (remaining=256)
[2026-06-03T20:22:48] Assigning confidence scores to events 
[2026-06-03T20:22:52] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:22:52] Writing fusions to file 'aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:22:53] Writing discarded fusions to file 'aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:23:29] Freeing resources
[2026-06-03T20:23:47] Done (elapsed time=00:12:56, CPU time=00:12:56, peak memory=16gb)