[2026-05-28T00:04:43] Launching Arriba 2.4.0
[2026-05-28T00:04:43] 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_00121_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3351805)
[2026-05-28T00:07:16] Marking multi-mapping alignments (marked=2121448)
[2026-05-28T00:07:18] Detecting strandedness (reverse)
[2026-05-28T00:07:18] Assigning strands to alignments 
[2026-05-28T00:07:19] Annotating alignments 
[2026-05-28T00:07:31] Filtering duplicates (remaining=2017747)
[2026-05-28T00:07:34] 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=1907186)
[2026-05-28T00:07:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1907186)
[2026-05-28T00:07:35] Filtering viral contigs with expression lower than the top 5 (remaining=1907186)
[2026-05-28T00:07:37] Filtering viral contigs with less than 5% coverage (remaining=1907186)
[2026-05-28T00:07:38] Estimating fragment length (mate gap mean=-86.8627, mate gap stddev=28.9635, read length mean=131.314)
[2026-05-28T00:07:38] Filtering read-through fragments with a distance <=10000bp (remaining=1770552)
[2026-05-28T00:07:39] Filtering inconsistently clipped mates (remaining=1735937)
[2026-05-28T00:07:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1689715)
[2026-05-28T00:07:41] Filtering fragments with small insert size (remaining=1689438)
[2026-05-28T00:07:42] Filtering alignments with long gaps (remaining=1689438)
[2026-05-28T00:07:42] Filtering fragments with both mates in the same gene (remaining=1689054)
[2026-05-28T00:07:43] Filtering fusions arising from hairpin structures (remaining=1580750)
[2026-05-28T00:07:44] Filtering reads with a mismatch p-value <=0.01 (remaining=704334)
[2026-05-28T00:07:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=331039)
[2026-05-28T00:07:52] Finding fusions and counting supporting reads (total=274224)
[2026-05-28T00:07:59] Merging adjacent fusion breakpoints (remaining=272669)
[2026-05-28T00:08:00] Filtering multi-mapping fusions by alignment score and read support (remaining=175611)
[2026-05-28T00:08:14] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:08:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=174429)
[2026-05-28T00:08:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=90925)
[2026-05-28T00:08:18] Filtering fusions with <2 supporting reads (remaining=13071)
[2026-05-28T00:08:18] Filtering fusions with an e-value >=0.3 (remaining=4495)
[2026-05-28T00:08:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4546)
[2026-05-28T00:08:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4511)
[2026-05-28T00:08:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4511)
[2026-05-28T00:08:20] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3154)
[2026-05-28T00:08:22] Searching for fusions with spliced split reads (remaining=3200)
[2026-05-28T00:08:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=2280)
[2026-05-28T00:08:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2255)
[2026-05-28T00:08:25] Searching for fusions with >=4 spliced events (remaining=2422)
[2026-05-28T00:08:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=626)
[2026-05-28T00:08:37] Filtering fusions with anchors <=23nt (remaining=525)
[2026-05-28T00:08:37] Filtering end-to-end fusions with low support (remaining=505)
[2026-05-28T00:08:38] Filtering fusions with no coverage around the breakpoints (remaining=492)
[2026-05-28T00:08:38] Indexing gene sequences 
[2026-05-28T00:08:42] Filtering genes with >=30% identity (remaining=220)
[2026-05-28T00:08:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=153)
[2026-05-28T00:08:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=147)
[2026-05-28T00:08:45] Searching for additional isoforms (remaining=169)
[2026-05-28T00:08:45] Assigning confidence scores to events 
[2026-05-28T00:08:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:08:47] Writing fusions to file 'tih_rna_sample_00121_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:08:48] Writing discarded fusions to file 'tih_rna_sample_00121_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:09:01] Freeing resources
[2026-05-28T00:09:08] Done (elapsed time=00:04:25, CPU time=00:04:23, peak memory=7.67gb)