[2026-06-03T19:39:32] Launching Arriba 2.4.0
[2026-06-03T19:39:32] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:39:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:39:46] Reading chimeric alignments from 'aih-tih-sc-e1cae1-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=7353366)
[2026-06-03T19:45:05] Marking multi-mapping alignments (marked=5259495)
[2026-06-03T19:45:09] Detecting strandedness (reverse)
[2026-06-03T19:45:09] Assigning strands to alignments 
[2026-06-03T19:45:12] Annotating alignments 
[2026-06-03T19:45:53] Filtering duplicates (remaining=3089632)
[2026-06-03T19:46:01] 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)
[2026-06-03T19:46:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2784184)
[2026-06-03T19:46:06] Filtering viral contigs with expression lower than the top 5 (remaining=2784184)
[2026-06-03T19:46:12] Filtering viral contigs with less than 5% coverage (remaining=2784184)
[2026-06-03T19:46:14] Estimating fragment length (mate gap mean=-82.7995, mate gap stddev=28.5219, read length mean=118.534)
[2026-06-03T19:46:14] Filtering read-through fragments with a distance <=10000bp (remaining=2679005)
[2026-06-03T19:46:17] Filtering inconsistently clipped mates (remaining=2602270)
[2026-06-03T19:46:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2456811)
[2026-06-03T19:46:23] Filtering fragments with small insert size (remaining=2455822)
[2026-06-03T19:46:25] Filtering alignments with long gaps (remaining=2455822)
[2026-06-03T19:46:27] Filtering fragments with both mates in the same gene (remaining=2455132)
[2026-06-03T19:46:29] Filtering fusions arising from hairpin structures (remaining=2270663)
[2026-06-03T19:46:32] Filtering reads with a mismatch p-value <=0.01 (remaining=836976)
[2026-06-03T19:46:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=364869)
[2026-06-03T19:46:46] Finding fusions and counting supporting reads (total=301799)
[2026-06-03T19:47:04] Merging adjacent fusion breakpoints (remaining=299431)
[2026-06-03T19:47:05] Filtering multi-mapping fusions by alignment score and read support (remaining=158404)
[2026-06-03T19:47:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T19:47:51] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=157434)
[2026-06-03T19:47:52] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=98352)
[2026-06-03T19:47:52] Filtering fusions with <2 supporting reads (remaining=10158)
[2026-06-03T19:47:53] Filtering fusions with an e-value >=0.3 (remaining=2713)
[2026-06-03T19:47:53] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2754)
[2026-06-03T19:47:57] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2672)
[2026-06-03T19:47:57] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2672)
[2026-06-03T19:47:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2648)
[2026-06-03T19:48:03] Searching for fusions with spliced split reads (remaining=2694)
[2026-06-03T19:48:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=2026)
[2026-06-03T19:48:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1972)
[2026-06-03T19:48:10] Searching for fusions with >=4 spliced events (remaining=2149)
[2026-06-03T19:48:11] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=606)
[2026-06-03T19:48:34] Filtering fusions with anchors <=23nt (remaining=477)
[2026-06-03T19:48:35] Filtering end-to-end fusions with low support (remaining=455)
[2026-06-03T19:48:35] Filtering fusions with no coverage around the breakpoints (remaining=436)
[2026-06-03T19:48:35] Indexing gene sequences 
[2026-06-03T19:48:40] Filtering genes with >=30% identity (remaining=125)
[2026-06-03T19:48:42] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=53)
[2026-06-03T19:48:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=53)
[2026-06-03T19:48:44] Searching for additional isoforms (remaining=63)
[2026-06-03T19:48:45] Assigning confidence scores to events 
[2026-06-03T19:48:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T19:48:48] Writing fusions to file 'aih-tih-sc-e1cae1-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T19:48:49] Writing discarded fusions to file 'aih-tih-sc-e1cae1-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T19:49:15] Freeing resources
[2026-06-03T19:49:33] Done (elapsed time=00:10:01, CPU time=00:10:00, peak memory=11.8gb)