[2026-06-08T08:50:13] Launching Arriba 2.4.0
[2026-06-08T08:50:13] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:50:23] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:50:28] Reading chimeric alignments from 'aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10988067)
[2026-06-08T08:57:35] Marking multi-mapping alignments (marked=7057980)
[2026-06-08T08:57:39] Detecting strandedness (reverse)
[2026-06-08T08:57:39] Assigning strands to alignments 
[2026-06-08T08:57:41] Annotating alignments 
[2026-06-08T08:58:17] Filtering duplicates (remaining=5927806)
[2026-06-08T08:58:24] 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=5605264)
[2026-06-08T08:58:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5605264)
[2026-06-08T08:58:28] Filtering viral contigs with expression lower than the top 5 (remaining=5605264)
[2026-06-08T08:58:32] Filtering viral contigs with less than 5% coverage (remaining=5605264)
[2026-06-08T08:58:35] Estimating fragment length (mate gap mean=-87.97, mate gap stddev=28.4336, read length mean=133.558)
[2026-06-08T08:58:35] Filtering read-through fragments with a distance <=10000bp (remaining=5374818)
[2026-06-08T08:58:37] Filtering inconsistently clipped mates (remaining=5309712)
[2026-06-08T08:58:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5176304)
[2026-06-08T08:58:43] Filtering fragments with small insert size (remaining=5175549)
[2026-06-08T08:58:45] Filtering alignments with long gaps (remaining=5175549)
[2026-06-08T08:58:47] Filtering fragments with both mates in the same gene (remaining=5174427)
[2026-06-08T08:58:49] Filtering fusions arising from hairpin structures (remaining=4988963)
[2026-06-08T08:58:52] Filtering reads with a mismatch p-value <=0.01 (remaining=2251896)
[2026-06-08T08:59:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=700275)
[2026-06-08T08:59:13] Finding fusions and counting supporting reads (total=495057)
[2026-06-08T08:59:29] Merging adjacent fusion breakpoints (remaining=490602)
[2026-06-08T08:59:30] Filtering multi-mapping fusions by alignment score and read support (remaining=308049)
[2026-06-08T09:00:04] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=306216)
[2026-06-08T09:00:11] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=185433)
[2026-06-08T09:00:12] Filtering fusions with <2 supporting reads (remaining=25279)
[2026-06-08T09:00:13] Filtering fusions with an e-value >=0.3 (remaining=6874)
[2026-06-08T09:00:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6917)
[2026-06-08T09:00:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6850)
[2026-06-08T09:00:18] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6850)
[2026-06-08T09:00:19] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6038)
[2026-06-08T09:00:24] Searching for fusions with spliced split reads (remaining=6142)
[2026-06-08T09:00:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=3971)
[2026-06-08T09:00:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3900)
[2026-06-08T09:00:31] Searching for fusions with >=4 spliced events (remaining=4398)
[2026-06-08T09:00:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1411)
[2026-06-08T09:00:47] Filtering fusions with anchors <=23nt (remaining=1134)
[2026-06-08T09:00:48] Filtering end-to-end fusions with low support (remaining=1092)
[2026-06-08T09:00:48] Filtering fusions with no coverage around the breakpoints (remaining=1061)
[2026-06-08T09:00:49] Indexing gene sequences 
[2026-06-08T09:00:54] Filtering genes with >=30% identity (remaining=376)
[2026-06-08T09:00:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=211)
[2026-06-08T09:00:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=197)
[2026-06-08T09:01:00] Searching for additional isoforms (remaining=242)
[2026-06-08T09:01:02] Assigning confidence scores to events 
[2026-06-08T09:01:05] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:05] Writing fusions to file 'aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:01:07] Writing discarded fusions to file 'aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:32] Freeing resources
[2026-06-08T09:01:49] Done (elapsed time=00:11:36, CPU time=00:11:34, peak memory=15.2gb)