[2026-06-08T08:45:39] Launching Arriba 2.4.0
[2026-06-08T08:45:39] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:45:49] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:45:53] Reading chimeric alignments from 'aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11271462)
[2026-06-08T08:52:58] Marking multi-mapping alignments (marked=7563525)
[2026-06-08T08:53:04] Detecting strandedness (reverse)
[2026-06-08T08:53:04] Assigning strands to alignments 
[2026-06-08T08:53:06] Annotating alignments 
[2026-06-08T08:53:50] Filtering duplicates (remaining=7113633)
[2026-06-08T08:54:00] 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=6611417)
[2026-06-08T08:54:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6611417)
[2026-06-08T08:54:05] Filtering viral contigs with expression lower than the top 5 (remaining=6611417)
[2026-06-08T08:54:10] Filtering viral contigs with less than 5% coverage (remaining=6611417)
[2026-06-08T08:54:13] Estimating fragment length (mate gap mean=-84.7075, mate gap stddev=28.9524, read length mean=125.479)
[2026-06-08T08:54:14] Filtering read-through fragments with a distance <=10000bp (remaining=6229026)
[2026-06-08T08:54:16] Filtering inconsistently clipped mates (remaining=6105918)
[2026-06-08T08:54:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5934107)
[2026-06-08T08:54:25] Filtering fragments with small insert size (remaining=5932897)
[2026-06-08T08:54:27] Filtering alignments with long gaps (remaining=5932897)
[2026-06-08T08:54:30] Filtering fragments with both mates in the same gene (remaining=5931706)
[2026-06-08T08:54:33] Filtering fusions arising from hairpin structures (remaining=5542487)
[2026-06-08T08:54:36] Filtering reads with a mismatch p-value <=0.01 (remaining=2265004)
[2026-06-08T08:54:52] Filtering reads with low entropy (k-mer content >=60%) (remaining=1134972)
[2026-06-08T08:55:04] Finding fusions and counting supporting reads (total=886188)
[2026-06-08T08:55:26] Merging adjacent fusion breakpoints (remaining=877964)
[2026-06-08T08:55:28] Filtering multi-mapping fusions by alignment score and read support (remaining=544608)
[2026-06-08T08:56:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:56:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=542514)
[2026-06-08T08:56:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=324701)
[2026-06-08T08:56:20] Filtering fusions with <2 supporting reads (remaining=35553)
[2026-06-08T08:56:21] Filtering fusions with an e-value >=0.3 (remaining=8402)
[2026-06-08T08:56:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8479)
[2026-06-08T08:56:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8354)
[2026-06-08T08:56:27] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8354)
[2026-06-08T08:56:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7508)
[2026-06-08T08:56:35] Searching for fusions with spliced split reads (remaining=7528)
[2026-06-08T08:56:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=4935)
[2026-06-08T08:56:43] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4870)
[2026-06-08T08:56:44] Searching for fusions with >=4 spliced events (remaining=6016)
[2026-06-08T08:56:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2394)
[2026-06-08T08:57:01] Filtering fusions with anchors <=23nt (remaining=1987)
[2026-06-08T08:57:02] Filtering end-to-end fusions with low support (remaining=1914)
[2026-06-08T08:57:03] Filtering fusions with no coverage around the breakpoints (remaining=1882)
[2026-06-08T08:57:04] Indexing gene sequences 
[2026-06-08T08:57:13] Filtering genes with >=30% identity (remaining=716)
[2026-06-08T08:57:18] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=420)
[2026-06-08T08:57:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=289)
[2026-06-08T08:57:31] Searching for additional isoforms (remaining=417)
[2026-06-08T08:57:32] Assigning confidence scores to events 
[2026-06-08T08:57:37] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:57:37] Writing fusions to file 'aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:57:42] Writing discarded fusions to file 'aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:58:21] Freeing resources
[2026-06-08T08:58:41] Done (elapsed time=00:13:02, CPU time=00:13:00, peak memory=16.2gb)