[2026-06-08T08:17:10] Launching Arriba 2.4.0
[2026-06-08T08:17:10] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:17:23] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:17:26] Reading chimeric alignments from 'aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11291517)
[2026-06-08T08:22:35] Marking multi-mapping alignments (marked=8360707)
[2026-06-08T08:22:39] Detecting strandedness (no)
[2026-06-08T08:22:39] Annotating alignments 
[2026-06-08T08:23:17] Filtering duplicates (remaining=4107030)
[2026-06-08T08:23:22] 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=3605252)
[2026-06-08T08:23:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3605252)
[2026-06-08T08:23:26] Filtering viral contigs with expression lower than the top 5 (remaining=3605252)
[2026-06-08T08:23:30] Filtering viral contigs with less than 5% coverage (remaining=3605252)
[2026-06-08T08:23:33] Estimating fragment length (mate gap mean=-81.9427, mate gap stddev=28.2591, read length mean=117.039)
[2026-06-08T08:23:33] Filtering read-through fragments with a distance <=10000bp (remaining=3448715)
[2026-06-08T08:23:35] Filtering inconsistently clipped mates (remaining=3359168)
[2026-06-08T08:23:37] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3197596)
[2026-06-08T08:23:41] Filtering fragments with small insert size (remaining=3196143)
[2026-06-08T08:23:43] Filtering alignments with long gaps (remaining=3196143)
[2026-06-08T08:23:45] Filtering fragments with both mates in the same gene (remaining=3195373)
[2026-06-08T08:23:47] Filtering fusions arising from hairpin structures (remaining=2998415)
[2026-06-08T08:23:50] Filtering reads with a mismatch p-value <=0.01 (remaining=1012388)
[2026-06-08T08:23:59] Filtering reads with low entropy (k-mer content >=60%) (remaining=432794)
[2026-06-08T08:24:07] Finding fusions and counting supporting reads (total=372869)
[2026-06-08T08:24:20] Merging adjacent fusion breakpoints (remaining=369847)
[2026-06-08T08:24:21] Filtering multi-mapping fusions by alignment score and read support (remaining=194406)
[2026-06-08T08:24:51] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:24:55] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=193281)
[2026-06-08T08:24:56] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=118338)
[2026-06-08T08:24:56] Filtering fusions with <2 supporting reads (remaining=10172)
[2026-06-08T08:24:57] Filtering fusions with an e-value >=0.3 (remaining=2506)
[2026-06-08T08:24:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2540)
[2026-06-08T08:25:01] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2468)
[2026-06-08T08:25:01] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2468)
[2026-06-08T08:25:02] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2421)
[2026-06-08T08:25:06] Searching for fusions with spliced split reads (remaining=2461)
[2026-06-08T08:25:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=1855)
[2026-06-08T08:25:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1837)
[2026-06-08T08:25:12] Searching for fusions with >=4 spliced events (remaining=2005)
[2026-06-08T08:25:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=727)
[2026-06-08T08:25:27] Filtering fusions with anchors <=23nt (remaining=572)
[2026-06-08T08:25:27] Filtering end-to-end fusions with low support (remaining=540)
[2026-06-08T08:25:28] Filtering fusions with no coverage around the breakpoints (remaining=525)
[2026-06-08T08:25:28] Indexing gene sequences 
[2026-06-08T08:25:32] Filtering genes with >=30% identity (remaining=200)
[2026-06-08T08:25:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=112)
[2026-06-08T08:25:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=109)
[2026-06-08T08:25:35] Searching for additional isoforms (remaining=126)
[2026-06-08T08:25:36] Assigning confidence scores to events 
[2026-06-08T08:25:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:25:38] Writing fusions to file 'aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:25:39] Writing discarded fusions to file 'aih-tih-sc-a97ce1-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:25:55] Freeing resources
[2026-06-08T08:26:11] Done (elapsed time=00:09:01, CPU time=00:08:59, peak memory=15.9gb)