[2026-06-08T08:48:21] Launching Arriba 2.4.0
[2026-06-08T08:48:21] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:31] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:37] Reading chimeric alignments from 'tih_rna_sample_00457_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10151681)
[2026-06-08T08:56:01] Marking multi-mapping alignments (marked=6334103)
[2026-06-08T08:56:06] Detecting strandedness (reverse)
[2026-06-08T08:56:06] Assigning strands to alignments 
[2026-06-08T08:56:08] Annotating alignments 
[2026-06-08T08:56:44] Filtering duplicates (remaining=4614251)
[2026-06-08T08:56:50] 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=4382263)
[2026-06-08T08:56:52] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4382263)
[2026-06-08T08:56:54] Filtering viral contigs with expression lower than the top 5 (remaining=4382263)
[2026-06-08T08:56:59] Filtering viral contigs with less than 5% coverage (remaining=4382263)
[2026-06-08T08:57:02] Estimating fragment length (mate gap mean=-87.6908, mate gap stddev=28.9166, read length mean=134.13)
[2026-06-08T08:57:02] Filtering read-through fragments with a distance <=10000bp (remaining=4111112)
[2026-06-08T08:57:04] Filtering inconsistently clipped mates (remaining=4056086)
[2026-06-08T08:57:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3947907)
[2026-06-08T08:57:11] Filtering fragments with small insert size (remaining=3947322)
[2026-06-08T08:57:13] Filtering alignments with long gaps (remaining=3947321)
[2026-06-08T08:57:15] Filtering fragments with both mates in the same gene (remaining=3946654)
[2026-06-08T08:57:17] Filtering fusions arising from hairpin structures (remaining=3774220)
[2026-06-08T08:57:20] Filtering reads with a mismatch p-value <=0.01 (remaining=1527731)
[2026-06-08T08:57:30] Filtering reads with low entropy (k-mer content >=60%) (remaining=631599)
[2026-06-08T08:57:39] Finding fusions and counting supporting reads (total=511626)
[2026-06-08T08:57:55] Merging adjacent fusion breakpoints (remaining=507839)
[2026-06-08T08:57:56] Filtering multi-mapping fusions by alignment score and read support (remaining=338349)
[2026-06-08T08:58:30] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=336722)
[2026-06-08T08:58:37] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=171968)
[2026-06-08T08:58:38] Filtering fusions with <2 supporting reads (remaining=24389)
[2026-06-08T08:58:38] Filtering fusions with an e-value >=0.3 (remaining=8085)
[2026-06-08T08:58:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8124)
[2026-06-08T08:58:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8061)
[2026-06-08T08:58:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8061)
[2026-06-08T08:58:44] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5120)
[2026-06-08T08:58:48] Searching for fusions with spliced split reads (remaining=5231)
[2026-06-08T08:58:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=3430)
[2026-06-08T08:58:54] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3375)
[2026-06-08T08:58:54] Searching for fusions with >=4 spliced events (remaining=3851)
[2026-06-08T08:58:56] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1338)
[2026-06-08T08:59:08] Filtering fusions with anchors <=23nt (remaining=1043)
[2026-06-08T08:59:09] Filtering end-to-end fusions with low support (remaining=1005)
[2026-06-08T08:59:09] Filtering fusions with no coverage around the breakpoints (remaining=983)
[2026-06-08T08:59:10] Indexing gene sequences 
[2026-06-08T08:59:14] Filtering genes with >=30% identity (remaining=332)
[2026-06-08T08:59:16] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=199)
[2026-06-08T08:59:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=190)
[2026-06-08T08:59:21] Searching for additional isoforms (remaining=227)
[2026-06-08T08:59:22] Assigning confidence scores to events 
[2026-06-08T08:59:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:25] Writing fusions to file 'tih_rna_sample_00457_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:26] Writing discarded fusions to file 'tih_rna_sample_00457_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:52] Freeing resources
[2026-06-08T09:00:08] Done (elapsed time=00:11:47, CPU time=00:11:46, peak memory=14.7gb)