[2026-05-28T00:06:47] Launching Arriba 2.4.0
[2026-05-28T00:06:47] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:06:56] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:07:00] Reading chimeric alignments from 'tih_rna_sample_00462_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3048375)
[2026-05-28T00:09:12] Marking multi-mapping alignments (marked=1848956)
[2026-05-28T00:09:13] Detecting strandedness (reverse)
[2026-05-28T00:09:13] Assigning strands to alignments 
[2026-05-28T00:09:14] Annotating alignments 
[2026-05-28T00:09:25] Filtering duplicates (remaining=2048813)
[2026-05-28T00:09:27] 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=1965971)
[2026-05-28T00:09:28] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1965971)
[2026-05-28T00:09:28] Filtering viral contigs with expression lower than the top 5 (remaining=1965971)
[2026-05-28T00:09:29] Filtering viral contigs with less than 5% coverage (remaining=1965971)
[2026-05-28T00:09:30] Estimating fragment length (mate gap mean=-87.5263, mate gap stddev=29.3229, read length mean=134.348)
[2026-05-28T00:09:30] Filtering read-through fragments with a distance <=10000bp (remaining=1819506)
[2026-05-28T00:09:31] Filtering inconsistently clipped mates (remaining=1790296)
[2026-05-28T00:09:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1752397)
[2026-05-28T00:09:33] Filtering fragments with small insert size (remaining=1752111)
[2026-05-28T00:09:33] Filtering alignments with long gaps (remaining=1752111)
[2026-05-28T00:09:34] Filtering fragments with both mates in the same gene (remaining=1751752)
[2026-05-28T00:09:35] Filtering fusions arising from hairpin structures (remaining=1650156)
[2026-05-28T00:09:35] Filtering reads with a mismatch p-value <=0.01 (remaining=757121)
[2026-05-28T00:09:40] Filtering reads with low entropy (k-mer content >=60%) (remaining=336728)
[2026-05-28T00:09:43] Finding fusions and counting supporting reads (total=285636)
[2026-05-28T00:09:49] Merging adjacent fusion breakpoints (remaining=283919)
[2026-05-28T00:09:50] Filtering multi-mapping fusions by alignment score and read support (remaining=195687)
[2026-05-28T00:10:02] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:10:04] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=194755)
[2026-05-28T00:10:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=95711)
[2026-05-28T00:10:05] Filtering fusions with <2 supporting reads (remaining=13580)
[2026-05-28T00:10:05] Filtering fusions with an e-value >=0.3 (remaining=4539)
[2026-05-28T00:10:06] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4569)
[2026-05-28T00:10:07] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4529)
[2026-05-28T00:10:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4529)
[2026-05-28T00:10:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3073)
[2026-05-28T00:10:10] Searching for fusions with spliced split reads (remaining=3100)
[2026-05-28T00:10:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=2218)
[2026-05-28T00:10:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2186)
[2026-05-28T00:10:13] Searching for fusions with >=4 spliced events (remaining=2386)
[2026-05-28T00:10:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=684)
[2026-05-28T00:10:31] Filtering fusions with anchors <=23nt (remaining=509)
[2026-05-28T00:10:31] Filtering end-to-end fusions with low support (remaining=495)
[2026-05-28T00:10:31] Filtering fusions with no coverage around the breakpoints (remaining=480)
[2026-05-28T00:10:32] Indexing gene sequences 
[2026-05-28T00:10:34] Filtering genes with >=30% identity (remaining=201)
[2026-05-28T00:10:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=125)
[2026-05-28T00:10:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=118)
[2026-05-28T00:10:37] Searching for additional isoforms (remaining=141)
[2026-05-28T00:10:38] Assigning confidence scores to events 
[2026-05-28T00:10:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:10:39] Writing fusions to file 'tih_rna_sample_00462_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:10:40] Writing discarded fusions to file 'tih_rna_sample_00462_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:10:51] Freeing resources
[2026-05-28T00:10:57] Done (elapsed time=00:04:10, CPU time=00:04:08, peak memory=7.37gb)