[2026-05-28T00:05:48] Launching Arriba 2.4.0
[2026-05-28T00:05:48] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:05:56] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:06:00] Reading chimeric alignments from 'tih_rna_sample_00166_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3303455)
[2026-05-28T00:08:12] Marking multi-mapping alignments (marked=2040785)
[2026-05-28T00:08:13] Detecting strandedness (reverse)
[2026-05-28T00:08:13] Assigning strands to alignments 
[2026-05-28T00:08:14] Annotating alignments 
[2026-05-28T00:08:25] Filtering duplicates (remaining=1917751)
[2026-05-28T00:08:27] 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=1853915)
[2026-05-28T00:08:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1853915)
[2026-05-28T00:08:28] Filtering viral contigs with expression lower than the top 5 (remaining=1853915)
[2026-05-28T00:08:29] Filtering viral contigs with less than 5% coverage (remaining=1853915)
[2026-05-28T00:08:30] Estimating fragment length (mate gap mean=-87.2366, mate gap stddev=28.4177, read length mean=133.478)
[2026-05-28T00:08:30] Filtering read-through fragments with a distance <=10000bp (remaining=1713923)
[2026-05-28T00:08:31] Filtering inconsistently clipped mates (remaining=1685288)
[2026-05-28T00:08:32] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1645557)
[2026-05-28T00:08:33] Filtering fragments with small insert size (remaining=1645309)
[2026-05-28T00:08:33] Filtering alignments with long gaps (remaining=1645309)
[2026-05-28T00:08:34] Filtering fragments with both mates in the same gene (remaining=1644988)
[2026-05-28T00:08:35] Filtering fusions arising from hairpin structures (remaining=1559939)
[2026-05-28T00:08:36] Filtering reads with a mismatch p-value <=0.01 (remaining=704080)
[2026-05-28T00:08:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=309126)
[2026-05-28T00:08:42] Finding fusions and counting supporting reads (total=262994)
[2026-05-28T00:08:48] Merging adjacent fusion breakpoints (remaining=261297)
[2026-05-28T00:08:48] Filtering multi-mapping fusions by alignment score and read support (remaining=170082)
[2026-05-28T00:08:59] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:09:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=169199)
[2026-05-28T00:09:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=79745)
[2026-05-28T00:09:02] Filtering fusions with <2 supporting reads (remaining=9791)
[2026-05-28T00:09:02] Filtering fusions with an e-value >=0.3 (remaining=2783)
[2026-05-28T00:09:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2822)
[2026-05-28T00:09:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2802)
[2026-05-28T00:09:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2802)
[2026-05-28T00:09:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2466)
[2026-05-28T00:09:06] Searching for fusions with spliced split reads (remaining=2497)
[2026-05-28T00:09:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=1849)
[2026-05-28T00:09:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1827)
[2026-05-28T00:09:08] Searching for fusions with >=4 spliced events (remaining=2032)
[2026-05-28T00:09:08] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=550)
[2026-05-28T00:09:19] Filtering fusions with anchors <=23nt (remaining=454)
[2026-05-28T00:09:19] Filtering end-to-end fusions with low support (remaining=450)
[2026-05-28T00:09:19] Filtering fusions with no coverage around the breakpoints (remaining=437)
[2026-05-28T00:09:20] Indexing gene sequences 
[2026-05-28T00:09:22] Filtering genes with >=30% identity (remaining=144)
[2026-05-28T00:09:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=90)
[2026-05-28T00:09:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=86)
[2026-05-28T00:09:24] Searching for additional isoforms (remaining=101)
[2026-05-28T00:09:24] Assigning confidence scores to events 
[2026-05-28T00:09:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:09:25] Writing fusions to file 'tih_rna_sample_00166_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:09:26] Writing discarded fusions to file 'tih_rna_sample_00166_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:09:36] Freeing resources
[2026-05-28T00:09:42] Done (elapsed time=00:03:54, CPU time=00:03:54, peak memory=7.57gb)