[2026-06-08T08:21:19] Launching Arriba 2.4.0
[2026-06-08T08:21:19] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:21:35] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:21:41] Reading chimeric alignments from 'tih_rna_sample_00666_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=12642013)
[2026-06-08T08:28:07] Marking multi-mapping alignments (marked=8931572)
[2026-06-08T08:28:13] Detecting strandedness (reverse)
[2026-06-08T08:28:13] Assigning strands to alignments 
[2026-06-08T08:28:15] Annotating alignments 
[2026-06-08T08:28:56] Filtering duplicates (remaining=4363838)
[2026-06-08T08:29:03] 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=3962058)
[2026-06-08T08:29:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3962058)
[2026-06-08T08:29:08] Filtering viral contigs with expression lower than the top 5 (remaining=3962058)
[2026-06-08T08:29:13] Filtering viral contigs with less than 5% coverage (remaining=3962058)
[2026-06-08T08:29:16] Estimating fragment length (mate gap mean=-83.3755, mate gap stddev=27.2573, read length mean=117.019)
[2026-06-08T08:29:16] Filtering read-through fragments with a distance <=10000bp (remaining=3782220)
[2026-06-08T08:29:18] Filtering inconsistently clipped mates (remaining=3700494)
[2026-06-08T08:29:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3603861)
[2026-06-08T08:29:25] Filtering fragments with small insert size (remaining=3602996)
[2026-06-08T08:29:27] Filtering alignments with long gaps (remaining=3602996)
[2026-06-08T08:29:30] Filtering fragments with both mates in the same gene (remaining=3602156)
[2026-06-08T08:29:32] Filtering fusions arising from hairpin structures (remaining=3400875)
[2026-06-08T08:29:35] Filtering reads with a mismatch p-value <=0.01 (remaining=1253286)
[2026-06-08T08:29:45] Filtering reads with low entropy (k-mer content >=60%) (remaining=417282)
[2026-06-08T08:29:53] Finding fusions and counting supporting reads (total=356945)
[2026-06-08T08:30:09] Merging adjacent fusion breakpoints (remaining=352134)
[2026-06-08T08:30:11] Filtering multi-mapping fusions by alignment score and read support (remaining=195509)
[2026-06-08T08:30:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:30:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=194735)
[2026-06-08T08:30:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=122312)
[2026-06-08T08:30:54] Filtering fusions with <2 supporting reads (remaining=11010)
[2026-06-08T08:30:54] Filtering fusions with an e-value >=0.3 (remaining=2486)
[2026-06-08T08:30:55] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2538)
[2026-06-08T08:30:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2481)
[2026-06-08T08:30:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2482)
[2026-06-08T08:31:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2482)
[2026-06-08T08:31:04] Searching for fusions with spliced split reads (remaining=2519)
[2026-06-08T08:31:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=1798)
[2026-06-08T08:31:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1784)
[2026-06-08T08:31:11] Searching for fusions with >=4 spliced events (remaining=2023)
[2026-06-08T08:31:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=931)
[2026-06-08T08:31:28] Filtering fusions with anchors <=23nt (remaining=785)
[2026-06-08T08:31:29] Filtering end-to-end fusions with low support (remaining=748)
[2026-06-08T08:31:29] Filtering fusions with no coverage around the breakpoints (remaining=723)
[2026-06-08T08:31:30] Indexing gene sequences 
[2026-06-08T08:31:34] Filtering genes with >=30% identity (remaining=195)
[2026-06-08T08:31:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=70)
[2026-06-08T08:31:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=67)
[2026-06-08T08:31:38] Searching for additional isoforms (remaining=79)
[2026-06-08T08:31:39] Assigning confidence scores to events 
[2026-06-08T08:31:41] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:31:41] Writing fusions to file 'tih_rna_sample_00666_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:31:42] Writing discarded fusions to file 'tih_rna_sample_00666_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:32:05] Freeing resources
[2026-06-08T08:32:24] Done (elapsed time=00:11:05, CPU time=00:11:04, peak memory=17.1gb)