[2026-06-08T08:28:17] Launching Arriba 2.4.0
[2026-06-08T08:28:17] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:28:26] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:28:30] Reading chimeric alignments from 'tih_rna_sample_00116_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=11839935)
[2026-06-08T08:34:41] Marking multi-mapping alignments (marked=7527721)
[2026-06-08T08:34:46] Detecting strandedness (reverse)
[2026-06-08T08:34:46] Assigning strands to alignments 
[2026-06-08T08:34:48] Annotating alignments 
[2026-06-08T08:35:27] Filtering duplicates (remaining=4829194)
[2026-06-08T08:35:33] 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=4560681)
[2026-06-08T08:35:35] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4560681)
[2026-06-08T08:35:37] Filtering viral contigs with expression lower than the top 5 (remaining=4560681)
[2026-06-08T08:35:42] Filtering viral contigs with less than 5% coverage (remaining=4560681)
[2026-06-08T08:35:45] Estimating fragment length (mate gap mean=-86.3641, mate gap stddev=26.9276, read length mean=124.083)
[2026-06-08T08:35:45] Filtering read-through fragments with a distance <=10000bp (remaining=4233899)
[2026-06-08T08:35:47] Filtering inconsistently clipped mates (remaining=4160917)
[2026-06-08T08:35:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4048600)
[2026-06-08T08:35:53] Filtering fragments with small insert size (remaining=4047543)
[2026-06-08T08:35:55] Filtering alignments with long gaps (remaining=4047543)
[2026-06-08T08:35:58] Filtering fragments with both mates in the same gene (remaining=4046650)
[2026-06-08T08:36:00] Filtering fusions arising from hairpin structures (remaining=3869117)
[2026-06-08T08:36:02] Filtering reads with a mismatch p-value <=0.01 (remaining=1501251)
[2026-06-08T08:36:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=702977)
[2026-06-08T08:36:20] Finding fusions and counting supporting reads (total=612305)
[2026-06-08T08:36:38] Merging adjacent fusion breakpoints (remaining=603507)
[2026-06-08T08:36:39] Filtering multi-mapping fusions by alignment score and read support (remaining=362293)
[2026-06-08T08:37:17] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:37:23] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=361190)
[2026-06-08T08:37:23] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=184851)
[2026-06-08T08:37:24] Filtering fusions with <2 supporting reads (remaining=20778)
[2026-06-08T08:37:25] Filtering fusions with an e-value >=0.3 (remaining=4916)
[2026-06-08T08:37:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4950)
[2026-06-08T08:37:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4868)
[2026-06-08T08:37:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4868)
[2026-06-08T08:37:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4750)
[2026-06-08T08:37:36] Searching for fusions with spliced split reads (remaining=4811)
[2026-06-08T08:37:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=3450)
[2026-06-08T08:37:42] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3404)
[2026-06-08T08:37:43] Searching for fusions with >=4 spliced events (remaining=3881)
[2026-06-08T08:37:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1627)
[2026-06-08T08:38:02] Filtering fusions with anchors <=23nt (remaining=1181)
[2026-06-08T08:38:02] Filtering end-to-end fusions with low support (remaining=1138)
[2026-06-08T08:38:03] Filtering fusions with no coverage around the breakpoints (remaining=1103)
[2026-06-08T08:38:04] Indexing gene sequences 
[2026-06-08T08:38:08] Filtering genes with >=30% identity (remaining=370)
[2026-06-08T08:38:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=118)
[2026-06-08T08:38:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=110)
[2026-06-08T08:38:14] Searching for additional isoforms (remaining=128)
[2026-06-08T08:38:15] Assigning confidence scores to events 
[2026-06-08T08:38:17] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:38:18] Writing fusions to file 'tih_rna_sample_00116_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:38:19] Writing discarded fusions to file 'tih_rna_sample_00116_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:38:43] Freeing resources
[2026-06-08T08:39:02] Done (elapsed time=00:10:45, CPU time=00:10:43, peak memory=16.4gb)