[2026-06-08T08:21:05] Launching Arriba 2.4.0
[2026-06-08T08:21:05] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:21:22] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:21:27] Reading chimeric alignments from 'tih_rna_sample_00479_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=6515769)
[2026-06-08T08:26:43] Marking multi-mapping alignments (marked=4068966)
[2026-06-08T08:26:46] Detecting strandedness (reverse)
[2026-06-08T08:26:46] Assigning strands to alignments 
[2026-06-08T08:26:48] Annotating alignments 
[2026-06-08T08:27:09] Filtering duplicates (remaining=4380855)
[2026-06-08T08:27:14] 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=4171008)
[2026-06-08T08:27:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4171008)
[2026-06-08T08:27:16] Filtering viral contigs with expression lower than the top 5 (remaining=4171008)
[2026-06-08T08:27:19] Filtering viral contigs with less than 5% coverage (remaining=4171008)
[2026-06-08T08:27:20] Estimating fragment length (mate gap mean=-87.2835, mate gap stddev=28.554, read length mean=133.551)
[2026-06-08T08:27:21] Filtering read-through fragments with a distance <=10000bp (remaining=3865797)
[2026-06-08T08:27:22] Filtering inconsistently clipped mates (remaining=3807096)
[2026-06-08T08:27:23] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3731567)
[2026-06-08T08:27:26] Filtering fragments with small insert size (remaining=3730826)
[2026-06-08T08:27:27] Filtering alignments with long gaps (remaining=3730826)
[2026-06-08T08:27:29] Filtering fragments with both mates in the same gene (remaining=3730150)
[2026-06-08T08:27:30] Filtering fusions arising from hairpin structures (remaining=3533516)
[2026-06-08T08:27:31] Filtering reads with a mismatch p-value <=0.01 (remaining=1635696)
[2026-06-08T08:27:41] Filtering reads with low entropy (k-mer content >=60%) (remaining=807397)
[2026-06-08T08:27:49] Finding fusions and counting supporting reads (total=626401)
[2026-06-08T08:28:01] Merging adjacent fusion breakpoints (remaining=621448)
[2026-06-08T08:28:02] Filtering multi-mapping fusions by alignment score and read support (remaining=392616)
[2026-06-08T08:28:23] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:28:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=389877)
[2026-06-08T08:28:29] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=212098)
[2026-06-08T08:28:29] Filtering fusions with <2 supporting reads (remaining=31551)
[2026-06-08T08:28:30] Filtering fusions with an e-value >=0.3 (remaining=8961)
[2026-06-08T08:28:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9017)
[2026-06-08T08:28:33] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8952)
[2026-06-08T08:28:33] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8952)
[2026-06-08T08:28:34] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6893)
[2026-06-08T08:28:38] Searching for fusions with spliced split reads (remaining=7022)
[2026-06-08T08:28:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=4414)
[2026-06-08T08:28:42] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4377)
[2026-06-08T08:28:42] Searching for fusions with >=4 spliced events (remaining=5189)
[2026-06-08T08:28:43] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1931)
[2026-06-08T08:28:59] Filtering fusions with anchors <=23nt (remaining=1689)
[2026-06-08T08:29:00] Filtering end-to-end fusions with low support (remaining=1651)
[2026-06-08T08:29:00] Filtering fusions with no coverage around the breakpoints (remaining=1610)
[2026-06-08T08:29:00] Indexing gene sequences 
[2026-06-08T08:29:09] Filtering genes with >=30% identity (remaining=623)
[2026-06-08T08:29:13] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=428)
[2026-06-08T08:29:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=329)
[2026-06-08T08:29:21] Searching for additional isoforms (remaining=474)
[2026-06-08T08:29:22] Assigning confidence scores to events 
[2026-06-08T08:29:24] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:29:24] Writing fusions to file 'tih_rna_sample_00479_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:29:29] Writing discarded fusions to file 'tih_rna_sample_00479_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:29:52] Freeing resources
[2026-06-08T08:30:04] Done (elapsed time=00:08:59, CPU time=00:08:57, peak memory=11.2gb)