[2026-06-08T09:07:25] Launching Arriba 2.4.0
[2026-06-08T09:07:25] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:07:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:07:42] Reading chimeric alignments from 'aih-tih-sc-cdd9d2-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9844117)
[2026-06-08T09:15:15] Marking multi-mapping alignments (marked=6150165)
[2026-06-08T09:15:18] Detecting strandedness (reverse)
[2026-06-08T09:15:18] Assigning strands to alignments 
[2026-06-08T09:15:20] Annotating alignments 
[2026-06-08T09:15:48] Filtering duplicates (remaining=5953040)
[2026-06-08T09:15:53] 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=5642646)
[2026-06-08T09:15:55] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5642646)
[2026-06-08T09:15:56] Filtering viral contigs with expression lower than the top 5 (remaining=5642646)
[2026-06-08T09:16:00] Filtering viral contigs with less than 5% coverage (remaining=5642646)
[2026-06-08T09:16:02] Estimating fragment length (mate gap mean=-87.184, mate gap stddev=29.8973, read length mean=135.949)
[2026-06-08T09:16:02] Filtering read-through fragments with a distance <=10000bp (remaining=5291046)
[2026-06-08T09:16:04] Filtering inconsistently clipped mates (remaining=5197143)
[2026-06-08T09:16:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5065734)
[2026-06-08T09:16:09] Filtering fragments with small insert size (remaining=5064926)
[2026-06-08T09:16:10] Filtering alignments with long gaps (remaining=5064925)
[2026-06-08T09:16:12] Filtering fragments with both mates in the same gene (remaining=5063983)
[2026-06-08T09:16:14] Filtering fusions arising from hairpin structures (remaining=4742208)
[2026-06-08T09:16:16] Filtering reads with a mismatch p-value <=0.01 (remaining=2247952)
[2026-06-08T09:16:28] Filtering reads with low entropy (k-mer content >=60%) (remaining=956957)
[2026-06-08T09:16:37] Finding fusions and counting supporting reads (total=720350)
[2026-06-08T09:16:51] Merging adjacent fusion breakpoints (remaining=713427)
[2026-06-08T09:16:53] Filtering multi-mapping fusions by alignment score and read support (remaining=466455)
[2026-06-08T09:17:18] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:17:23] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=463310)
[2026-06-08T09:17:24] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=249075)
[2026-06-08T09:17:25] Filtering fusions with <2 supporting reads (remaining=34715)
[2026-06-08T09:17:26] Filtering fusions with an e-value >=0.3 (remaining=12523)
[2026-06-08T09:17:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12608)
[2026-06-08T09:17:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12542)
[2026-06-08T09:17:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12542)
[2026-06-08T09:17:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7110)
[2026-06-08T09:17:35] Searching for fusions with spliced split reads (remaining=7145)
[2026-06-08T09:17:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=4137)
[2026-06-08T09:17:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4071)
[2026-06-08T09:17:41] Searching for fusions with >=4 spliced events (remaining=4876)
[2026-06-08T09:17:42] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2033)
[2026-06-08T09:17:56] Filtering fusions with anchors <=23nt (remaining=1683)
[2026-06-08T09:17:56] Filtering end-to-end fusions with low support (remaining=1631)
[2026-06-08T09:17:57] Filtering fusions with no coverage around the breakpoints (remaining=1596)
[2026-06-08T09:17:57] Indexing gene sequences 
[2026-06-08T09:18:04] Filtering genes with >=30% identity (remaining=697)
[2026-06-08T09:18:08] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=495)
[2026-06-08T09:18:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=390)
[2026-06-08T09:18:19] Searching for additional isoforms (remaining=529)
[2026-06-08T09:18:20] Assigning confidence scores to events 
[2026-06-08T09:18:23] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:18:23] Writing fusions to file 'aih-tih-sc-cdd9d2-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:18:26] Writing discarded fusions to file 'aih-tih-sc-cdd9d2-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:18:49] Freeing resources
[2026-06-08T09:19:04] Done (elapsed time=00:11:39, CPU time=00:11:37, peak memory=14.5gb)