[2026-06-08T08:20:20] Launching Arriba 2.4.0
[2026-06-08T08:20:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:20:28] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:20:32] Reading chimeric alignments from 'aih-tih-sc-3282fd-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10166462)
[2026-06-08T08:25:56] Marking multi-mapping alignments (marked=7021581)
[2026-06-08T08:26:00] Detecting strandedness (reverse)
[2026-06-08T08:26:00] Assigning strands to alignments 
[2026-06-08T08:26:02] Annotating alignments 
[2026-06-08T08:26:36] Filtering duplicates (remaining=5479558)
[2026-06-08T08:26:42] 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=4983921)
[2026-06-08T08:26:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4983921)
[2026-06-08T08:26:45] Filtering viral contigs with expression lower than the top 5 (remaining=4983921)
[2026-06-08T08:26:49] Filtering viral contigs with less than 5% coverage (remaining=4983921)
[2026-06-08T08:26:52] Estimating fragment length (mate gap mean=-83.0484, mate gap stddev=27.9406, read length mean=117.585)
[2026-06-08T08:26:52] Filtering read-through fragments with a distance <=10000bp (remaining=4660029)
[2026-06-08T08:26:54] Filtering inconsistently clipped mates (remaining=4564715)
[2026-06-08T08:26:56] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4422589)
[2026-06-08T08:26:59] Filtering fragments with small insert size (remaining=4421416)
[2026-06-08T08:27:01] Filtering alignments with long gaps (remaining=4421416)
[2026-06-08T08:27:03] Filtering fragments with both mates in the same gene (remaining=4420269)
[2026-06-08T08:27:05] Filtering fusions arising from hairpin structures (remaining=4171873)
[2026-06-08T08:27:07] Filtering reads with a mismatch p-value <=0.01 (remaining=1582954)
[2026-06-08T08:27:18] Filtering reads with low entropy (k-mer content >=60%) (remaining=786725)
[2026-06-08T08:27:26] Finding fusions and counting supporting reads (total=650118)
[2026-06-08T08:27:42] Merging adjacent fusion breakpoints (remaining=641622)
[2026-06-08T08:27:44] Filtering multi-mapping fusions by alignment score and read support (remaining=362527)
[2026-06-08T08:28:16] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:28:23] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=361336)
[2026-06-08T08:28:23] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=216883)
[2026-06-08T08:28:24] Filtering fusions with <2 supporting reads (remaining=22159)
[2026-06-08T08:28:25] Filtering fusions with an e-value >=0.3 (remaining=5022)
[2026-06-08T08:28:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5068)
[2026-06-08T08:28:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4969)
[2026-06-08T08:28:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4969)
[2026-06-08T08:28:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4908)
[2026-06-08T08:28:36] Searching for fusions with spliced split reads (remaining=4964)
[2026-06-08T08:28:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=3425)
[2026-06-08T08:28:42] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3362)
[2026-06-08T08:28:43] Searching for fusions with >=4 spliced events (remaining=3905)
[2026-06-08T08:28:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1600)
[2026-06-08T08:28:58] Filtering fusions with anchors <=23nt (remaining=1313)
[2026-06-08T08:28:59] Filtering end-to-end fusions with low support (remaining=1253)
[2026-06-08T08:28:59] Filtering fusions with no coverage around the breakpoints (remaining=1232)
[2026-06-08T08:29:00] Indexing gene sequences 
[2026-06-08T08:29:04] Filtering genes with >=30% identity (remaining=348)
[2026-06-08T08:29:06] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=128)
[2026-06-08T08:29:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=128)
[2026-06-08T08:29:10] Searching for additional isoforms (remaining=152)
[2026-06-08T08:29:11] Assigning confidence scores to events 
[2026-06-08T08:29:14] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:29:14] Writing fusions to file 'aih-tih-sc-3282fd-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:29:15] Writing discarded fusions to file 'aih-tih-sc-3282fd-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:29:43] Freeing resources
[2026-06-08T08:29:59] Done (elapsed time=00:09:39, CPU time=00:09:38, peak memory=14.9gb)