[2026-06-08T08:27:09] Launching Arriba 2.4.0
[2026-06-08T08:27:09] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:27:17] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:21] Reading chimeric alignments from 'tih_rna_sample_00158_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=8170534)
[2026-06-08T08:32:17] Marking multi-mapping alignments (marked=5387611)
[2026-06-08T08:32:20] Detecting strandedness (reverse)
[2026-06-08T08:32:20] Assigning strands to alignments 
[2026-06-08T08:32:22] Annotating alignments 
[2026-06-08T08:32:48] Filtering duplicates (remaining=2759845)
[2026-06-08T08:32:51] 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=2542789)
[2026-06-08T08:32:53] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2542789)
[2026-06-08T08:32:54] Filtering viral contigs with expression lower than the top 5 (remaining=2542789)
[2026-06-08T08:32:57] Filtering viral contigs with less than 5% coverage (remaining=2542789)
[2026-06-08T08:32:59] Estimating fragment length (mate gap mean=-86.4731, mate gap stddev=30.0765, read length mean=133.203)
[2026-06-08T08:32:59] Filtering read-through fragments with a distance <=10000bp (remaining=2418410)
[2026-06-08T08:33:01] Filtering inconsistently clipped mates (remaining=2378702)
[2026-06-08T08:33:02] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2272107)
[2026-06-08T08:33:04] Filtering fragments with small insert size (remaining=2271680)
[2026-06-08T08:33:06] Filtering alignments with long gaps (remaining=2271680)
[2026-06-08T08:33:07] Filtering fragments with both mates in the same gene (remaining=2271285)
[2026-06-08T08:33:09] Filtering fusions arising from hairpin structures (remaining=2175848)
[2026-06-08T08:33:11] Filtering reads with a mismatch p-value <=0.01 (remaining=890442)
[2026-06-08T08:33:17] Filtering reads with low entropy (k-mer content >=60%) (remaining=306995)
[2026-06-08T08:33:22] Finding fusions and counting supporting reads (total=257638)
[2026-06-08T08:33:32] Merging adjacent fusion breakpoints (remaining=255833)
[2026-06-08T08:33:33] Filtering multi-mapping fusions by alignment score and read support (remaining=144207)
[2026-06-08T08:33:58] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:34:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=142662)
[2026-06-08T08:34:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=85810)
[2026-06-08T08:34:02] Filtering fusions with <2 supporting reads (remaining=9805)
[2026-06-08T08:34:02] Filtering fusions with an e-value >=0.3 (remaining=3080)
[2026-06-08T08:34:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3101)
[2026-06-08T08:34:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3042)
[2026-06-08T08:34:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3042)
[2026-06-08T08:34:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2443)
[2026-06-08T08:34:09] Searching for fusions with spliced split reads (remaining=2564)
[2026-06-08T08:34:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=1799)
[2026-06-08T08:34:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1775)
[2026-06-08T08:34:13] Searching for fusions with >=4 spliced events (remaining=1938)
[2026-06-08T08:34:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=525)
[2026-06-08T08:34:26] Filtering fusions with anchors <=23nt (remaining=404)
[2026-06-08T08:34:26] Filtering end-to-end fusions with low support (remaining=389)
[2026-06-08T08:34:26] Filtering fusions with no coverage around the breakpoints (remaining=377)
[2026-06-08T08:34:27] Indexing gene sequences 
[2026-06-08T08:34:29] Filtering genes with >=30% identity (remaining=133)
[2026-06-08T08:34:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=67)
[2026-06-08T08:34:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=67)
[2026-06-08T08:34:31] Searching for additional isoforms (remaining=76)
[2026-06-08T08:34:32] Assigning confidence scores to events 
[2026-06-08T08:34:34] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:34:34] Writing fusions to file 'tih_rna_sample_00158_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:34:34] Writing discarded fusions to file 'tih_rna_sample_00158_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:34:48] Freeing resources
[2026-06-08T08:35:00] Done (elapsed time=00:07:51, CPU time=00:07:50, peak memory=12.5gb)