[2026-06-08T08:16:42] Launching Arriba 2.4.0
[2026-06-08T08:16:42] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:16:57] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:17:01] Reading chimeric alignments from 'tih_rna_sample_00218_23H5VFLT4_s10.Aligned.sortedByCoord.out.bam' (total=9785092)
[2026-06-08T08:25:49] Marking multi-mapping alignments (marked=6219274)
[2026-06-08T08:25:54] Detecting strandedness (reverse)
[2026-06-08T08:25:54] Assigning strands to alignments 
[2026-06-08T08:25:56] Annotating alignments 
[2026-06-08T08:26:35] Filtering duplicates (remaining=6660477)
[2026-06-08T08:26:43] 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=6228902)
[2026-06-08T08:26:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6228902)
[2026-06-08T08:26:48] Filtering viral contigs with expression lower than the top 5 (remaining=6228902)
[2026-06-08T08:26:53] Filtering viral contigs with less than 5% coverage (remaining=6228902)
[2026-06-08T08:26:55] Estimating fragment length (mate gap mean=-87.0717, mate gap stddev=30.1469, read length mean=130.994)
[2026-06-08T08:26:55] Filtering read-through fragments with a distance <=10000bp (remaining=5777881)
[2026-06-08T08:26:58] Filtering inconsistently clipped mates (remaining=5650475)
[2026-06-08T08:27:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5344428)
[2026-06-08T08:27:06] Filtering fragments with small insert size (remaining=5343083)
[2026-06-08T08:27:08] Filtering alignments with long gaps (remaining=5343083)
[2026-06-08T08:27:10] Filtering fragments with both mates in the same gene (remaining=5341748)
[2026-06-08T08:27:13] Filtering fusions arising from hairpin structures (remaining=4890509)
[2026-06-08T08:27:15] Filtering reads with a mismatch p-value <=0.01 (remaining=2159739)
[2026-06-08T08:27:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=1439358)
[2026-06-08T08:27:43] Finding fusions and counting supporting reads (total=1168119)
[2026-06-08T08:28:03] Merging adjacent fusion breakpoints (remaining=1159754)
[2026-06-08T08:28:05] Filtering multi-mapping fusions by alignment score and read support (remaining=726026)
[2026-06-08T08:28:39] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:28:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=724042)
[2026-06-08T08:28:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=465962)
[2026-06-08T08:28:49] Filtering fusions with <2 supporting reads (remaining=39467)
[2026-06-08T08:28:50] Filtering fusions with an e-value >=0.3 (remaining=8150)
[2026-06-08T08:28:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8218)
[2026-06-08T08:28:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8099)
[2026-06-08T08:28:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8099)
[2026-06-08T08:28:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7336)
[2026-06-08T08:29:03] Searching for fusions with spliced split reads (remaining=7371)
[2026-06-08T08:29:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=4517)
[2026-06-08T08:29:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4458)
[2026-06-08T08:29:11] Searching for fusions with >=4 spliced events (remaining=5718)
[2026-06-08T08:29:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2435)
[2026-06-08T08:29:30] Filtering fusions with anchors <=23nt (remaining=1965)
[2026-06-08T08:29:31] Filtering end-to-end fusions with low support (remaining=1926)
[2026-06-08T08:29:32] Filtering fusions with no coverage around the breakpoints (remaining=1911)
[2026-06-08T08:29:32] Indexing gene sequences 
[2026-06-08T08:29:41] Filtering genes with >=30% identity (remaining=601)
[2026-06-08T08:29:46] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=309)
[2026-06-08T08:29:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=253)
[2026-06-08T08:29:59] Searching for additional isoforms (remaining=360)
[2026-06-08T08:30:01] Assigning confidence scores to events 
[2026-06-08T08:30:06] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:30:06] Writing fusions to file 'tih_rna_sample_00218_23H5VFLT4_s10.arriba.fusions.tsv' 
[2026-06-08T08:30:10] Writing discarded fusions to file 'tih_rna_sample_00218_23H5VFLT4_s10.arriba.fusions.discarded.tsv'
[2026-06-08T08:30:55] Freeing resources
[2026-06-08T08:31:18] Done (elapsed time=00:14:36, CPU time=00:14:35, peak memory=15.1gb)