[2026-06-08T08:33:19] Launching Arriba 2.4.0
[2026-06-08T08:33:19] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:33:31] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:33:34] Reading chimeric alignments from 'tih_rna_sample_00090_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=14291956)
[2026-06-08T08:40:19] Marking multi-mapping alignments (marked=9975093)
[2026-06-08T08:40:24] Detecting strandedness (reverse)
[2026-06-08T08:40:24] Assigning strands to alignments 
[2026-06-08T08:40:26] Annotating alignments 
[2026-06-08T08:41:07] Filtering duplicates (remaining=4795120)
[2026-06-08T08:41:13] 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=4333199)
[2026-06-08T08:41:16] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4333199)
[2026-06-08T08:41:18] Filtering viral contigs with expression lower than the top 5 (remaining=4333199)
[2026-06-08T08:41:24] Filtering viral contigs with less than 5% coverage (remaining=4333199)
[2026-06-08T08:41:26] Estimating fragment length (mate gap mean=-84.6853, mate gap stddev=27.6746, read length mean=123.235)
[2026-06-08T08:41:26] Filtering read-through fragments with a distance <=10000bp (remaining=4081498)
[2026-06-08T08:41:29] Filtering inconsistently clipped mates (remaining=4001453)
[2026-06-08T08:41:32] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3813403)
[2026-06-08T08:41:36] Filtering fragments with small insert size (remaining=3812033)
[2026-06-08T08:41:38] Filtering alignments with long gaps (remaining=3812033)
[2026-06-08T08:41:41] Filtering fragments with both mates in the same gene (remaining=3811186)
[2026-06-08T08:41:44] Filtering fusions arising from hairpin structures (remaining=3629043)
[2026-06-08T08:41:47] Filtering reads with a mismatch p-value <=0.01 (remaining=1375091)
[2026-06-08T08:41:57] Filtering reads with low entropy (k-mer content >=60%) (remaining=552154)
[2026-06-08T08:42:06] Finding fusions and counting supporting reads (total=480905)
[2026-06-08T08:42:23] Merging adjacent fusion breakpoints (remaining=474540)
[2026-06-08T08:42:24] Filtering multi-mapping fusions by alignment score and read support (remaining=262379)
[2026-06-08T08:43:03] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:43:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=260908)
[2026-06-08T08:43:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=145588)
[2026-06-08T08:43:09] Filtering fusions with <2 supporting reads (remaining=14144)
[2026-06-08T08:43:09] Filtering fusions with an e-value >=0.3 (remaining=3257)
[2026-06-08T08:43:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3287)
[2026-06-08T08:43:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3205)
[2026-06-08T08:43:14] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3205)
[2026-06-08T08:43:15] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3091)
[2026-06-08T08:43:20] Searching for fusions with spliced split reads (remaining=3136)
[2026-06-08T08:43:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=2216)
[2026-06-08T08:43:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2198)
[2026-06-08T08:43:27] Searching for fusions with >=4 spliced events (remaining=2505)
[2026-06-08T08:43:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1067)
[2026-06-08T08:43:41] Filtering fusions with anchors <=23nt (remaining=861)
[2026-06-08T08:43:42] Filtering end-to-end fusions with low support (remaining=826)
[2026-06-08T08:43:42] Filtering fusions with no coverage around the breakpoints (remaining=801)
[2026-06-08T08:43:43] Indexing gene sequences 
[2026-06-08T08:43:46] Filtering genes with >=30% identity (remaining=263)
[2026-06-08T08:43:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=63)
[2026-06-08T08:43:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=57)
[2026-06-08T08:43:49] Searching for additional isoforms (remaining=70)
[2026-06-08T08:43:50] Assigning confidence scores to events 
[2026-06-08T08:43:52] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:43:52] Writing fusions to file 'tih_rna_sample_00090_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:43:53] Writing discarded fusions to file 'tih_rna_sample_00090_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:44:13] Freeing resources
[2026-06-08T08:44:33] Done (elapsed time=00:11:14, CPU time=00:11:13, peak memory=18.8gb)