[2026-06-08T08:26:49] Launching Arriba 2.4.0
[2026-06-08T08:26:49] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:27:03] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:08] Reading chimeric alignments from 'aih-tih-sc-7fc50e-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=7505108)
[2026-06-08T08:32:07] Marking multi-mapping alignments (marked=5028362)
[2026-06-08T08:32:10] Detecting strandedness (reverse)
[2026-06-08T08:32:10] Assigning strands to alignments 
[2026-06-08T08:32:12] Annotating alignments 
[2026-06-08T08:32:36] Filtering duplicates (remaining=4162131)
[2026-06-08T08:32:41] 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=3912178)
[2026-06-08T08:32:42] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3912178)
[2026-06-08T08:32:43] Filtering viral contigs with expression lower than the top 5 (remaining=3912178)
[2026-06-08T08:32:47] Filtering viral contigs with less than 5% coverage (remaining=3912178)
[2026-06-08T08:32:49] Estimating fragment length (mate gap mean=-85.646, mate gap stddev=28.89, read length mean=127.125)
[2026-06-08T08:32:49] Filtering read-through fragments with a distance <=10000bp (remaining=3749897)
[2026-06-08T08:32:50] Filtering inconsistently clipped mates (remaining=3686414)
[2026-06-08T08:32:52] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3556211)
[2026-06-08T08:32:55] Filtering fragments with small insert size (remaining=3555727)
[2026-06-08T08:32:56] Filtering alignments with long gaps (remaining=3555727)
[2026-06-08T08:32:58] Filtering fragments with both mates in the same gene (remaining=3554970)
[2026-06-08T08:32:59] Filtering fusions arising from hairpin structures (remaining=3380769)
[2026-06-08T08:33:01] Filtering reads with a mismatch p-value <=0.01 (remaining=1546282)
[2026-06-08T08:33:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=492845)
[2026-06-08T08:33:17] Finding fusions and counting supporting reads (total=371890)
[2026-06-08T08:33:29] Merging adjacent fusion breakpoints (remaining=368458)
[2026-06-08T08:33:30] Filtering multi-mapping fusions by alignment score and read support (remaining=213237)
[2026-06-08T08:33:53] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:33:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=212234)
[2026-06-08T08:33:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=126250)
[2026-06-08T08:33:59] Filtering fusions with <2 supporting reads (remaining=16322)
[2026-06-08T08:33:59] Filtering fusions with an e-value >=0.3 (remaining=4560)
[2026-06-08T08:33:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4611)
[2026-06-08T08:34:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4517)
[2026-06-08T08:34:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4517)
[2026-06-08T08:34:03] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4044)
[2026-06-08T08:34:07] Searching for fusions with spliced split reads (remaining=4102)
[2026-06-08T08:34:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=2969)
[2026-06-08T08:34:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2927)
[2026-06-08T08:34:11] Searching for fusions with >=4 spliced events (remaining=3239)
[2026-06-08T08:34:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1073)
[2026-06-08T08:34:31] Filtering fusions with anchors <=23nt (remaining=891)
[2026-06-08T08:34:31] Filtering end-to-end fusions with low support (remaining=863)
[2026-06-08T08:34:32] Filtering fusions with no coverage around the breakpoints (remaining=836)
[2026-06-08T08:34:32] Indexing gene sequences 
[2026-06-08T08:34:36] Filtering genes with >=30% identity (remaining=301)
[2026-06-08T08:34:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=186)
[2026-06-08T08:34:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=173)
[2026-06-08T08:34:43] Searching for additional isoforms (remaining=192)
[2026-06-08T08:34:44] Assigning confidence scores to events 
[2026-06-08T08:34:46] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:34:46] Writing fusions to file 'aih-tih-sc-7fc50e-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:34:48] Writing discarded fusions to file 'aih-tih-sc-7fc50e-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:35:09] Freeing resources
[2026-06-08T08:35:21] Done (elapsed time=00:08:32, CPU time=00:08:31, peak memory=11.8gb)