[2026-06-08T08:12:05] Launching Arriba 2.4.0
[2026-06-08T08:12:05] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:12:19] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:12:24] Reading chimeric alignments from 'tih_rna_sample_00451_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=6427248)
[2026-06-08T08:16:58] Marking multi-mapping alignments (marked=4063822)
[2026-06-08T08:17:00] Detecting strandedness (reverse)
[2026-06-08T08:17:00] Assigning strands to alignments 
[2026-06-08T08:17:01] Annotating alignments 
[2026-06-08T08:17:21] Filtering duplicates (remaining=4261269)
[2026-06-08T08:17:25] 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=4110300)
[2026-06-08T08:17:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4110300)
[2026-06-08T08:17:27] Filtering viral contigs with expression lower than the top 5 (remaining=4110300)
[2026-06-08T08:17:30] Filtering viral contigs with less than 5% coverage (remaining=4110300)
[2026-06-08T08:17:32] Estimating fragment length (mate gap mean=-87.7154, mate gap stddev=28.0001, read length mean=129.383)
[2026-06-08T08:17:32] Filtering read-through fragments with a distance <=10000bp (remaining=3731147)
[2026-06-08T08:17:33] Filtering inconsistently clipped mates (remaining=3661040)
[2026-06-08T08:17:34] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3574004)
[2026-06-08T08:17:37] Filtering fragments with small insert size (remaining=3573361)
[2026-06-08T08:17:38] Filtering alignments with long gaps (remaining=3573361)
[2026-06-08T08:17:40] Filtering fragments with both mates in the same gene (remaining=3572629)
[2026-06-08T08:17:41] Filtering fusions arising from hairpin structures (remaining=3364272)
[2026-06-08T08:17:42] Filtering reads with a mismatch p-value <=0.01 (remaining=1501870)
[2026-06-08T08:17:52] Filtering reads with low entropy (k-mer content >=60%) (remaining=799425)
[2026-06-08T08:18:00] Finding fusions and counting supporting reads (total=656553)
[2026-06-08T08:18:10] Merging adjacent fusion breakpoints (remaining=650685)
[2026-06-08T08:18:12] Filtering multi-mapping fusions by alignment score and read support (remaining=395757)
[2026-06-08T08:18:31] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:18:35] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=393614)
[2026-06-08T08:18:35] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=212849)
[2026-06-08T08:18:36] Filtering fusions with <2 supporting reads (remaining=26111)
[2026-06-08T08:18:37] Filtering fusions with an e-value >=0.3 (remaining=6425)
[2026-06-08T08:18:37] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6476)
[2026-06-08T08:18:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6412)
[2026-06-08T08:18:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6412)
[2026-06-08T08:18:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6058)
[2026-06-08T08:18:44] Searching for fusions with spliced split reads (remaining=6174)
[2026-06-08T08:18:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=4075)
[2026-06-08T08:18:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4020)
[2026-06-08T08:18:48] Searching for fusions with >=4 spliced events (remaining=4804)
[2026-06-08T08:18:49] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1911)
[2026-06-08T08:19:02] Filtering fusions with anchors <=23nt (remaining=1650)
[2026-06-08T08:19:02] Filtering end-to-end fusions with low support (remaining=1606)
[2026-06-08T08:19:03] Filtering fusions with no coverage around the breakpoints (remaining=1560)
[2026-06-08T08:19:03] Indexing gene sequences 
[2026-06-08T08:19:09] Filtering genes with >=30% identity (remaining=462)
[2026-06-08T08:19:11] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=229)
[2026-06-08T08:19:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=212)
[2026-06-08T08:19:14] Searching for additional isoforms (remaining=277)
[2026-06-08T08:19:15] Assigning confidence scores to events 
[2026-06-08T08:19:17] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:19:18] Writing fusions to file 'tih_rna_sample_00451_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:19:20] Writing discarded fusions to file 'tih_rna_sample_00451_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:19:42] Freeing resources
[2026-06-08T08:19:53] Done (elapsed time=00:07:48, CPU time=00:07:47, peak memory=11gb)