[2026-06-08T08:10:07] Launching Arriba 2.4.0
[2026-06-08T08:10:07] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:10:16] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:10:20] Reading chimeric alignments from 'aih-tih-sc-e1cae1-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=7353366)
[2026-06-08T08:14:15] Marking multi-mapping alignments (marked=5259495)
[2026-06-08T08:14:17] Detecting strandedness (reverse)
[2026-06-08T08:14:17] Assigning strands to alignments 
[2026-06-08T08:14:19] Annotating alignments 
[2026-06-08T08:14:43] Filtering duplicates (remaining=3089632)
[2026-06-08T08:14:47] 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=2784184)
[2026-06-08T08:14:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2784184)
[2026-06-08T08:14:50] Filtering viral contigs with expression lower than the top 5 (remaining=2784184)
[2026-06-08T08:14:52] Filtering viral contigs with less than 5% coverage (remaining=2784184)
[2026-06-08T08:14:54] Estimating fragment length (mate gap mean=-82.7995, mate gap stddev=28.5219, read length mean=118.534)
[2026-06-08T08:14:54] Filtering read-through fragments with a distance <=10000bp (remaining=2679005)
[2026-06-08T08:14:56] Filtering inconsistently clipped mates (remaining=2602270)
[2026-06-08T08:14:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2456811)
[2026-06-08T08:15:00] Filtering fragments with small insert size (remaining=2455822)
[2026-06-08T08:15:01] Filtering alignments with long gaps (remaining=2455822)
[2026-06-08T08:15:02] Filtering fragments with both mates in the same gene (remaining=2455132)
[2026-06-08T08:15:04] Filtering fusions arising from hairpin structures (remaining=2270663)
[2026-06-08T08:15:05] Filtering reads with a mismatch p-value <=0.01 (remaining=836976)
[2026-06-08T08:15:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=364869)
[2026-06-08T08:15:17] Finding fusions and counting supporting reads (total=301799)
[2026-06-08T08:15:27] Merging adjacent fusion breakpoints (remaining=299431)
[2026-06-08T08:15:28] Filtering multi-mapping fusions by alignment score and read support (remaining=158404)
[2026-06-08T08:15:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:15:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=157434)
[2026-06-08T08:15:56] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=98352)
[2026-06-08T08:15:57] Filtering fusions with <2 supporting reads (remaining=10158)
[2026-06-08T08:15:57] Filtering fusions with an e-value >=0.3 (remaining=2713)
[2026-06-08T08:15:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2754)
[2026-06-08T08:16:00] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2672)
[2026-06-08T08:16:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2672)
[2026-06-08T08:16:01] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2648)
[2026-06-08T08:16:04] Searching for fusions with spliced split reads (remaining=2694)
[2026-06-08T08:16:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=2026)
[2026-06-08T08:16:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1972)
[2026-06-08T08:16:08] Searching for fusions with >=4 spliced events (remaining=2149)
[2026-06-08T08:16:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=606)
[2026-06-08T08:16:21] Filtering fusions with anchors <=23nt (remaining=477)
[2026-06-08T08:16:22] Filtering end-to-end fusions with low support (remaining=455)
[2026-06-08T08:16:22] Filtering fusions with no coverage around the breakpoints (remaining=436)
[2026-06-08T08:16:23] Indexing gene sequences 
[2026-06-08T08:16:25] Filtering genes with >=30% identity (remaining=125)
[2026-06-08T08:16:26] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=53)
[2026-06-08T08:16:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=53)
[2026-06-08T08:16:28] Searching for additional isoforms (remaining=63)
[2026-06-08T08:16:28] Assigning confidence scores to events 
[2026-06-08T08:16:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:16:30] Writing fusions to file 'aih-tih-sc-e1cae1-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:16:31] Writing discarded fusions to file 'aih-tih-sc-e1cae1-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:16:47] Freeing resources
[2026-06-08T08:16:58] Done (elapsed time=00:06:51, CPU time=00:06:49, peak memory=11.8gb)