[2026-05-28T00:04:42] Launching Arriba 2.4.0
[2026-05-28T00:04:42] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:04:52] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:04:56] Reading chimeric alignments from 'tih_rna_sample_00124_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3239535)
[2026-05-28T00:07:50] Marking multi-mapping alignments (marked=1976806)
[2026-05-28T00:07:52] Detecting strandedness (reverse)
[2026-05-28T00:07:52] Assigning strands to alignments 
[2026-05-28T00:07:52] Annotating alignments 
[2026-05-28T00:08:07] Filtering duplicates (remaining=1992178)
[2026-05-28T00:08:09] 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=1914000)
[2026-05-28T00:08:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1914000)
[2026-05-28T00:08:10] Filtering viral contigs with expression lower than the top 5 (remaining=1914000)
[2026-05-28T00:08:11] Filtering viral contigs with less than 5% coverage (remaining=1914000)
[2026-05-28T00:08:12] Estimating fragment length (mate gap mean=-86.6214, mate gap stddev=29.2325, read length mean=131.325)
[2026-05-28T00:08:12] Filtering read-through fragments with a distance <=10000bp (remaining=1771738)
[2026-05-28T00:08:13] Filtering inconsistently clipped mates (remaining=1741692)
[2026-05-28T00:08:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1697976)
[2026-05-28T00:08:15] Filtering fragments with small insert size (remaining=1697569)
[2026-05-28T00:08:16] Filtering alignments with long gaps (remaining=1697569)
[2026-05-28T00:08:17] Filtering fragments with both mates in the same gene (remaining=1697252)
[2026-05-28T00:08:17] Filtering fusions arising from hairpin structures (remaining=1603247)
[2026-05-28T00:08:18] Filtering reads with a mismatch p-value <=0.01 (remaining=708580)
[2026-05-28T00:08:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=340790)
[2026-05-28T00:08:26] Finding fusions and counting supporting reads (total=280320)
[2026-05-28T00:08:32] Merging adjacent fusion breakpoints (remaining=277638)
[2026-05-28T00:08:33] Filtering multi-mapping fusions by alignment score and read support (remaining=182534)
[2026-05-28T00:08:44] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:08:46] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=181573)
[2026-05-28T00:08:47] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=90208)
[2026-05-28T00:08:47] Filtering fusions with <2 supporting reads (remaining=13290)
[2026-05-28T00:08:47] Filtering fusions with an e-value >=0.3 (remaining=4216)
[2026-05-28T00:08:47] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4258)
[2026-05-28T00:08:49] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4220)
[2026-05-28T00:08:49] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4220)
[2026-05-28T00:08:49] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3334)
[2026-05-28T00:08:51] Searching for fusions with spliced split reads (remaining=3396)
[2026-05-28T00:08:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=2389)
[2026-05-28T00:08:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2327)
[2026-05-28T00:08:54] Searching for fusions with >=4 spliced events (remaining=2485)
[2026-05-28T00:08:54] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=643)
[2026-05-28T00:09:07] Filtering fusions with anchors <=23nt (remaining=492)
[2026-05-28T00:09:07] Filtering end-to-end fusions with low support (remaining=474)
[2026-05-28T00:09:08] Filtering fusions with no coverage around the breakpoints (remaining=460)
[2026-05-28T00:09:08] Indexing gene sequences 
[2026-05-28T00:09:11] Filtering genes with >=30% identity (remaining=189)
[2026-05-28T00:09:11] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=131)
[2026-05-28T00:09:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=131)
[2026-05-28T00:09:13] Searching for additional isoforms (remaining=148)
[2026-05-28T00:09:14] Assigning confidence scores to events 
[2026-05-28T00:09:15] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:09:15] Writing fusions to file 'tih_rna_sample_00124_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:09:16] Writing discarded fusions to file 'tih_rna_sample_00124_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:09:28] Freeing resources
[2026-05-28T00:09:37] Done (elapsed time=00:04:55, CPU time=00:04:54, peak memory=7.56gb)