[2026-06-08T08:20:05] Launching Arriba 2.4.0
[2026-06-08T08:20:05] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:20:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:20:22] Reading chimeric alignments from 'tih_rna_sample_00163_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=5906310)
[2026-06-08T08:24:46] Marking multi-mapping alignments (marked=3702826)
[2026-06-08T08:24:48] Detecting strandedness (reverse)
[2026-06-08T08:24:48] Assigning strands to alignments 
[2026-06-08T08:24:49] Annotating alignments 
[2026-06-08T08:25:06] Filtering duplicates (remaining=3200799)
[2026-06-08T08:25:09] 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=3062736)
[2026-06-08T08:25:10] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3062736)
[2026-06-08T08:25:10] Filtering viral contigs with expression lower than the top 5 (remaining=3062736)
[2026-06-08T08:25:13] Filtering viral contigs with less than 5% coverage (remaining=3062736)
[2026-06-08T08:25:14] Estimating fragment length (mate gap mean=-88.0649, mate gap stddev=29.3855, read length mean=135.558)
[2026-06-08T08:25:14] Filtering read-through fragments with a distance <=10000bp (remaining=2861629)
[2026-06-08T08:25:15] Filtering inconsistently clipped mates (remaining=2817677)
[2026-06-08T08:25:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2739784)
[2026-06-08T08:25:18] Filtering fragments with small insert size (remaining=2739364)
[2026-06-08T08:25:18] Filtering alignments with long gaps (remaining=2739364)
[2026-06-08T08:25:19] Filtering fragments with both mates in the same gene (remaining=2738761)
[2026-06-08T08:25:20] Filtering fusions arising from hairpin structures (remaining=2588505)
[2026-06-08T08:25:22] Filtering reads with a mismatch p-value <=0.01 (remaining=1158248)
[2026-06-08T08:25:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=503795)
[2026-06-08T08:25:32] Finding fusions and counting supporting reads (total=413510)
[2026-06-08T08:25:40] Merging adjacent fusion breakpoints (remaining=410166)
[2026-06-08T08:25:41] Filtering multi-mapping fusions by alignment score and read support (remaining=257694)
[2026-06-08T08:25:56] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:25:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=255819)
[2026-06-08T08:26:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=133974)
[2026-06-08T08:26:00] Filtering fusions with <2 supporting reads (remaining=18770)
[2026-06-08T08:26:01] Filtering fusions with an e-value >=0.3 (remaining=6864)
[2026-06-08T08:26:01] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6901)
[2026-06-08T08:26:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6866)
[2026-06-08T08:26:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6866)
[2026-06-08T08:26:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4294)
[2026-06-08T08:26:06] Searching for fusions with spliced split reads (remaining=4353)
[2026-06-08T08:26:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=2906)
[2026-06-08T08:26:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2871)
[2026-06-08T08:26:10] Searching for fusions with >=4 spliced events (remaining=3200)
[2026-06-08T08:26:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1061)
[2026-06-08T08:26:23] Filtering fusions with anchors <=23nt (remaining=874)
[2026-06-08T08:26:23] Filtering end-to-end fusions with low support (remaining=847)
[2026-06-08T08:26:24] Filtering fusions with no coverage around the breakpoints (remaining=827)
[2026-06-08T08:26:24] Indexing gene sequences 
[2026-06-08T08:26:28] Filtering genes with >=30% identity (remaining=304)
[2026-06-08T08:26:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=162)
[2026-06-08T08:26:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=145)
[2026-06-08T08:26:41] Searching for additional isoforms (remaining=192)
[2026-06-08T08:26:41] Assigning confidence scores to events 
[2026-06-08T08:26:43] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:26:43] Writing fusions to file 'tih_rna_sample_00163_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:26:44] Writing discarded fusions to file 'tih_rna_sample_00163_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:26:58] Freeing resources
[2026-06-08T08:27:07] Done (elapsed time=00:07:02, CPU time=00:07:01, peak memory=10.3gb)