[2026-06-08T08:20:53] Launching Arriba 2.4.0
[2026-06-08T08:20:53] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:21:09] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:21:13] Reading chimeric alignments from 'tih_rna_sample_00164_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=8561814)
[2026-06-08T08:25:19] Marking multi-mapping alignments (marked=6238895)
[2026-06-08T08:25:23] Detecting strandedness (reverse)
[2026-06-08T08:25:23] Assigning strands to alignments 
[2026-06-08T08:25:24] Annotating alignments 
[2026-06-08T08:25:54] Filtering duplicates (remaining=3064523)
[2026-06-08T08:25:59] 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=2672203)
[2026-06-08T08:26:00] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2672203)
[2026-06-08T08:26:02] Filtering viral contigs with expression lower than the top 5 (remaining=2672203)
[2026-06-08T08:26:06] Filtering viral contigs with less than 5% coverage (remaining=2672203)
[2026-06-08T08:26:08] Estimating fragment length (mate gap mean=-88.8561, mate gap stddev=27.6742, read length mean=124.553)
[2026-06-08T08:26:08] Filtering read-through fragments with a distance <=10000bp (remaining=2582596)
[2026-06-08T08:26:10] Filtering inconsistently clipped mates (remaining=2542358)
[2026-06-08T08:26:11] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2484468)
[2026-06-08T08:26:14] Filtering fragments with small insert size (remaining=2483737)
[2026-06-08T08:26:16] Filtering alignments with long gaps (remaining=2483737)
[2026-06-08T08:26:18] Filtering fragments with both mates in the same gene (remaining=2483386)
[2026-06-08T08:26:20] Filtering fusions arising from hairpin structures (remaining=2372668)
[2026-06-08T08:26:22] Filtering reads with a mismatch p-value <=0.01 (remaining=686179)
[2026-06-08T08:26:28] Filtering reads with low entropy (k-mer content >=60%) (remaining=309356)
[2026-06-08T08:26:34] Finding fusions and counting supporting reads (total=261887)
[2026-06-08T08:26:46] Merging adjacent fusion breakpoints (remaining=258941)
[2026-06-08T08:26:47] Filtering multi-mapping fusions by alignment score and read support (remaining=151305)
[2026-06-08T08:27:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:27:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=150600)
[2026-06-08T08:27:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=90833)
[2026-06-08T08:27:18] Filtering fusions with <2 supporting reads (remaining=8726)
[2026-06-08T08:27:18] Filtering fusions with an e-value >=0.3 (remaining=1808)
[2026-06-08T08:27:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1826)
[2026-06-08T08:27:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1786)
[2026-06-08T08:27:21] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1786)
[2026-06-08T08:27:22] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1630)
[2026-06-08T08:27:25] Searching for fusions with spliced split reads (remaining=1732)
[2026-06-08T08:27:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=1373)
[2026-06-08T08:27:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1365)
[2026-06-08T08:27:29] Searching for fusions with >=4 spliced events (remaining=1479)
[2026-06-08T08:27:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=627)
[2026-06-08T08:27:44] Filtering fusions with anchors <=23nt (remaining=408)
[2026-06-08T08:27:45] Filtering end-to-end fusions with low support (remaining=351)
[2026-06-08T08:27:45] Filtering fusions with no coverage around the breakpoints (remaining=335)
[2026-06-08T08:27:45] Indexing gene sequences 
[2026-06-08T08:27:48] Filtering genes with >=30% identity (remaining=102)
[2026-06-08T08:27:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=61)
[2026-06-08T08:27:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=61)
[2026-06-08T08:27:50] Searching for additional isoforms (remaining=66)
[2026-06-08T08:27:51] Assigning confidence scores to events 
[2026-06-08T08:27:52] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:27:52] Writing fusions to file 'tih_rna_sample_00164_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:27:53] Writing discarded fusions to file 'tih_rna_sample_00164_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:28:09] Freeing resources
[2026-06-08T08:28:23] Done (elapsed time=00:07:30, CPU time=00:07:29, peak memory=13.2gb)