[2026-06-08T08:48:27] Launching Arriba 2.4.0
[2026-06-08T08:48:27] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:37] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:42] Reading chimeric alignments from 'tih_rna_sample_00480_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=10530505)
[2026-06-08T08:55:21] Marking multi-mapping alignments (marked=7041235)
[2026-06-08T08:55:25] Detecting strandedness (reverse)
[2026-06-08T08:55:25] Assigning strands to alignments 
[2026-06-08T08:55:27] Annotating alignments 
[2026-06-08T08:56:02] Filtering duplicates (remaining=5630919)
[2026-06-08T08:56:09] 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=5284944)
[2026-06-08T08:56:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5284944)
[2026-06-08T08:56:13] Filtering viral contigs with expression lower than the top 5 (remaining=5284944)
[2026-06-08T08:56:17] Filtering viral contigs with less than 5% coverage (remaining=5284944)
[2026-06-08T08:56:19] Estimating fragment length (mate gap mean=-87.5002, mate gap stddev=28.2837, read length mean=130.837)
[2026-06-08T08:56:20] Filtering read-through fragments with a distance <=10000bp (remaining=4976051)
[2026-06-08T08:56:22] Filtering inconsistently clipped mates (remaining=4886103)
[2026-06-08T08:56:24] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4738926)
[2026-06-08T08:56:28] Filtering fragments with small insert size (remaining=4738186)
[2026-06-08T08:56:30] Filtering alignments with long gaps (remaining=4738186)
[2026-06-08T08:56:32] Filtering fragments with both mates in the same gene (remaining=4737178)
[2026-06-08T08:56:34] Filtering fusions arising from hairpin structures (remaining=4449354)
[2026-06-08T08:56:36] Filtering reads with a mismatch p-value <=0.01 (remaining=1942111)
[2026-06-08T08:56:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=829070)
[2026-06-08T08:56:57] Finding fusions and counting supporting reads (total=654831)
[2026-06-08T08:57:14] Merging adjacent fusion breakpoints (remaining=649646)
[2026-06-08T08:57:15] Filtering multi-mapping fusions by alignment score and read support (remaining=392502)
[2026-06-08T08:57:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:55] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=390576)
[2026-06-08T08:57:55] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=222302)
[2026-06-08T08:57:56] Filtering fusions with <2 supporting reads (remaining=27292)
[2026-06-08T08:57:57] Filtering fusions with an e-value >=0.3 (remaining=7251)
[2026-06-08T08:57:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7294)
[2026-06-08T08:58:01] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7208)
[2026-06-08T08:58:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7208)
[2026-06-08T08:58:03] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6526)
[2026-06-08T08:58:08] Searching for fusions with spliced split reads (remaining=6641)
[2026-06-08T08:58:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=4436)
[2026-06-08T08:58:14] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4387)
[2026-06-08T08:58:14] Searching for fusions with >=4 spliced events (remaining=5403)
[2026-06-08T08:58:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2382)
[2026-06-08T08:58:30] Filtering fusions with anchors <=23nt (remaining=1999)
[2026-06-08T08:58:30] Filtering end-to-end fusions with low support (remaining=1959)
[2026-06-08T08:58:31] Filtering fusions with no coverage around the breakpoints (remaining=1917)
[2026-06-08T08:58:32] Indexing gene sequences 
[2026-06-08T08:58:40] Filtering genes with >=30% identity (remaining=784)
[2026-06-08T08:58:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=479)
[2026-06-08T08:58:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=332)
[2026-06-08T08:58:50] Searching for additional isoforms (remaining=452)
[2026-06-08T08:58:51] Assigning confidence scores to events 
[2026-06-08T08:58:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:55] Writing fusions to file 'tih_rna_sample_00480_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:58:57] Writing discarded fusions to file 'tih_rna_sample_00480_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:23] Freeing resources
[2026-06-08T08:59:40] Done (elapsed time=00:11:13, CPU time=00:11:11, peak memory=15.2gb)