[2026-05-28T00:04:56] Launching Arriba 2.4.0
[2026-05-28T00:04:56] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:05:05] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:05:09] Reading chimeric alignments from 'tih_rna_sample_00150_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=3210542)
[2026-05-28T00:07:23] Marking multi-mapping alignments (marked=1978220)
[2026-05-28T00:07:24] Detecting strandedness (reverse)
[2026-05-28T00:07:24] Assigning strands to alignments 
[2026-05-28T00:07:25] Annotating alignments 
[2026-05-28T00:07:37] Filtering duplicates (remaining=2432729)
[2026-05-28T00:07:39] 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=2328074)
[2026-05-28T00:07:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2328074)
[2026-05-28T00:07:41] Filtering viral contigs with expression lower than the top 5 (remaining=2328074)
[2026-05-28T00:07:42] Filtering viral contigs with less than 5% coverage (remaining=2328074)
[2026-05-28T00:07:43] Estimating fragment length (mate gap mean=-87.5283, mate gap stddev=28.3849, read length mean=132.782)
[2026-05-28T00:07:43] Filtering read-through fragments with a distance <=10000bp (remaining=2142451)
[2026-05-28T00:07:44] Filtering inconsistently clipped mates (remaining=2107346)
[2026-05-28T00:07:44] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2066141)
[2026-05-28T00:07:46] Filtering fragments with small insert size (remaining=2065898)
[2026-05-28T00:07:46] Filtering alignments with long gaps (remaining=2065898)
[2026-05-28T00:07:47] Filtering fragments with both mates in the same gene (remaining=2065505)
[2026-05-28T00:07:48] Filtering fusions arising from hairpin structures (remaining=1944595)
[2026-05-28T00:07:49] Filtering reads with a mismatch p-value <=0.01 (remaining=911563)
[2026-05-28T00:07:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=465075)
[2026-05-28T00:07:57] Finding fusions and counting supporting reads (total=360538)
[2026-05-28T00:08:04] Merging adjacent fusion breakpoints (remaining=358204)
[2026-05-28T00:08:05] Filtering multi-mapping fusions by alignment score and read support (remaining=237709)
[2026-05-28T00:08:16] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:08:19] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=236862)
[2026-05-28T00:08:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=124938)
[2026-05-28T00:08:20] Filtering fusions with <2 supporting reads (remaining=17150)
[2026-05-28T00:08:20] Filtering fusions with an e-value >=0.3 (remaining=4765)
[2026-05-28T00:08:20] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4801)
[2026-05-28T00:08:22] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4785)
[2026-05-28T00:08:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4785)
[2026-05-28T00:08:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4266)
[2026-05-28T00:08:24] Searching for fusions with spliced split reads (remaining=4309)
[2026-05-28T00:08:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=2958)
[2026-05-28T00:08:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2939)
[2026-05-28T00:08:27] Searching for fusions with >=4 spliced events (remaining=3239)
[2026-05-28T00:08:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=972)
[2026-05-28T00:08:39] Filtering fusions with anchors <=23nt (remaining=766)
[2026-05-28T00:08:40] Filtering end-to-end fusions with low support (remaining=740)
[2026-05-28T00:08:40] Filtering fusions with no coverage around the breakpoints (remaining=713)
[2026-05-28T00:08:40] Indexing gene sequences 
[2026-05-28T00:08:43] Filtering genes with >=30% identity (remaining=264)
[2026-05-28T00:08:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=148)
[2026-05-28T00:08:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=142)
[2026-05-28T00:08:47] Searching for additional isoforms (remaining=158)
[2026-05-28T00:08:48] Assigning confidence scores to events 
[2026-05-28T00:08:49] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:08:49] Writing fusions to file 'tih_rna_sample_00150_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-05-28T00:08:50] Writing discarded fusions to file 'tih_rna_sample_00150_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T00:09:04] Freeing resources
[2026-05-28T00:09:10] Done (elapsed time=00:04:14, CPU time=00:04:13, peak memory=7.59gb)