[2026-06-08T08:47:28] Launching Arriba 2.4.0
[2026-06-08T08:47:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:40] Reading chimeric alignments from 'tih_rna_sample_00150_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=9736221)
[2026-06-08T08:54:15] Marking multi-mapping alignments (marked=6013316)
[2026-06-08T08:54:19] Detecting strandedness (reverse)
[2026-06-08T08:54:19] Assigning strands to alignments 
[2026-06-08T08:54:21] Annotating alignments 
[2026-06-08T08:54:53] Filtering duplicates (remaining=5911818)
[2026-06-08T08:55:00] 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=5652912)
[2026-06-08T08:55:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5652912)
[2026-06-08T08:55:04] Filtering viral contigs with expression lower than the top 5 (remaining=5652912)
[2026-06-08T08:55:08] Filtering viral contigs with less than 5% coverage (remaining=5652912)
[2026-06-08T08:55:10] Estimating fragment length (mate gap mean=-87.601, mate gap stddev=28.3629, read length mean=132.965)
[2026-06-08T08:55:11] Filtering read-through fragments with a distance <=10000bp (remaining=5232601)
[2026-06-08T08:55:13] Filtering inconsistently clipped mates (remaining=5152530)
[2026-06-08T08:55:15] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5035693)
[2026-06-08T08:55:20] Filtering fragments with small insert size (remaining=5035035)
[2026-06-08T08:55:22] Filtering alignments with long gaps (remaining=5035035)
[2026-06-08T08:55:25] Filtering fragments with both mates in the same gene (remaining=5034110)
[2026-06-08T08:55:27] Filtering fusions arising from hairpin structures (remaining=4766110)
[2026-06-08T08:55:30] Filtering reads with a mismatch p-value <=0.01 (remaining=2148837)
[2026-06-08T08:55:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=1071644)
[2026-06-08T08:55:53] Finding fusions and counting supporting reads (total=782482)
[2026-06-08T08:56:12] Merging adjacent fusion breakpoints (remaining=775320)
[2026-06-08T08:56:13] Filtering multi-mapping fusions by alignment score and read support (remaining=508450)
[2026-06-08T08:56:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:56:55] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=506765)
[2026-06-08T08:56:56] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=268921)
[2026-06-08T08:56:57] Filtering fusions with <2 supporting reads (remaining=38083)
[2026-06-08T08:56:58] Filtering fusions with an e-value >=0.3 (remaining=9862)
[2026-06-08T08:56:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9901)
[2026-06-08T08:57:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9830)
[2026-06-08T08:57:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9830)
[2026-06-08T08:57:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8448)
[2026-06-08T08:57:10] Searching for fusions with spliced split reads (remaining=8546)
[2026-06-08T08:57:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=5217)
[2026-06-08T08:57:16] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5170)
[2026-06-08T08:57:17] Searching for fusions with >=4 spliced events (remaining=6207)
[2026-06-08T08:57:18] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2305)
[2026-06-08T08:57:33] Filtering fusions with anchors <=23nt (remaining=1877)
[2026-06-08T08:57:33] Filtering end-to-end fusions with low support (remaining=1817)
[2026-06-08T08:57:34] Filtering fusions with no coverage around the breakpoints (remaining=1773)
[2026-06-08T08:57:35] Indexing gene sequences 
[2026-06-08T08:57:41] Filtering genes with >=30% identity (remaining=537)
[2026-06-08T08:57:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=211)
[2026-06-08T08:57:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=193)
[2026-06-08T08:57:49] Searching for additional isoforms (remaining=232)
[2026-06-08T08:57:50] Assigning confidence scores to events 
[2026-06-08T08:57:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:57:54] Writing fusions to file 'tih_rna_sample_00150_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:57:56] Writing discarded fusions to file 'tih_rna_sample_00150_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:58:28] Freeing resources
[2026-06-08T08:58:45] Done (elapsed time=00:11:17, CPU time=00:11:16, peak memory=14.5gb)