[2026-06-08T08:25:43] Launching Arriba 2.4.0
[2026-06-08T08:25:43] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:25:57] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:26:01] Reading chimeric alignments from 'tih_rna_sample_00280_23H5VFLT4_s18.Aligned.sortedByCoord.out.bam' (total=10563816)
[2026-06-08T08:33:46] Marking multi-mapping alignments (marked=7078879)
[2026-06-08T08:33:50] Detecting strandedness (reverse)
[2026-06-08T08:33:50] Assigning strands to alignments 
[2026-06-08T08:33:52] Annotating alignments 
[2026-06-08T08:34:24] Filtering duplicates (remaining=6815758)
[2026-06-08T08:34:31] 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=6272973)
[2026-06-08T08:34:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6272973)
[2026-06-08T08:34:35] Filtering viral contigs with expression lower than the top 5 (remaining=6272973)
[2026-06-08T08:34:39] Filtering viral contigs with less than 5% coverage (remaining=6272973)
[2026-06-08T08:34:41] Estimating fragment length (mate gap mean=-86.7256, mate gap stddev=30.7116, read length mean=132.25)
[2026-06-08T08:34:41] Filtering read-through fragments with a distance <=10000bp (remaining=5823517)
[2026-06-08T08:34:43] Filtering inconsistently clipped mates (remaining=5703914)
[2026-06-08T08:34:45] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5284774)
[2026-06-08T08:34:50] Filtering fragments with small insert size (remaining=5283481)
[2026-06-08T08:34:52] Filtering alignments with long gaps (remaining=5283481)
[2026-06-08T08:34:54] Filtering fragments with both mates in the same gene (remaining=5282176)
[2026-06-08T08:34:56] Filtering fusions arising from hairpin structures (remaining=4776703)
[2026-06-08T08:34:59] Filtering reads with a mismatch p-value <=0.01 (remaining=2143672)
[2026-06-08T08:35:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=1298985)
[2026-06-08T08:35:23] Finding fusions and counting supporting reads (total=1044530)
[2026-06-08T08:35:40] Merging adjacent fusion breakpoints (remaining=1036254)
[2026-06-08T08:35:42] Filtering multi-mapping fusions by alignment score and read support (remaining=638629)
[2026-06-08T08:36:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:36:21] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=635431)
[2026-06-08T08:36:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=395464)
[2026-06-08T08:36:23] Filtering fusions with <2 supporting reads (remaining=36217)
[2026-06-08T08:36:24] Filtering fusions with an e-value >=0.3 (remaining=9538)
[2026-06-08T08:36:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9629)
[2026-06-08T08:36:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9462)
[2026-06-08T08:36:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9462)
[2026-06-08T08:36:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6384)
[2026-06-08T08:36:36] Searching for fusions with spliced split reads (remaining=6400)
[2026-06-08T08:36:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=3848)
[2026-06-08T08:36:42] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3814)
[2026-06-08T08:36:43] Searching for fusions with >=4 spliced events (remaining=4678)
[2026-06-08T08:36:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1870)
[2026-06-08T08:37:00] Filtering fusions with anchors <=23nt (remaining=1482)
[2026-06-08T08:37:01] Filtering end-to-end fusions with low support (remaining=1433)
[2026-06-08T08:37:01] Filtering fusions with no coverage around the breakpoints (remaining=1407)
[2026-06-08T08:37:02] Indexing gene sequences 
[2026-06-08T08:37:07] Filtering genes with >=30% identity (remaining=434)
[2026-06-08T08:37:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=189)
[2026-06-08T08:37:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=171)
[2026-06-08T08:37:15] Searching for additional isoforms (remaining=248)
[2026-06-08T08:37:16] Assigning confidence scores to events 
[2026-06-08T08:37:19] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:37:20] Writing fusions to file 'tih_rna_sample_00280_23H5VFLT4_s18.arriba.fusions.tsv' 
[2026-06-08T08:37:22] Writing discarded fusions to file 'tih_rna_sample_00280_23H5VFLT4_s18.arriba.fusions.discarded.tsv'
[2026-06-08T08:37:52] Freeing resources
[2026-06-08T08:38:09] Done (elapsed time=00:12:26, CPU time=00:12:25, peak memory=15.9gb)