[2026-05-28T00:04:59] Launching Arriba 2.4.0
[2026-05-28T00:04:59] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:05:07] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:05:11] Reading chimeric alignments from 'tih_rna_sample_00461_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=3782220)
[2026-05-28T00:07:37] Marking multi-mapping alignments (marked=2490614)
[2026-05-28T00:07:39] Detecting strandedness (reverse)
[2026-05-28T00:07:39] Assigning strands to alignments 
[2026-05-28T00:07:39] Annotating alignments 
[2026-05-28T00:07:53] Filtering duplicates (remaining=2744791)
[2026-05-28T00:07:56] 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=2600765)
[2026-05-28T00:07:57] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2600765)
[2026-05-28T00:07:57] Filtering viral contigs with expression lower than the top 5 (remaining=2600765)
[2026-05-28T00:07:59] Filtering viral contigs with less than 5% coverage (remaining=2600765)
[2026-05-28T00:08:00] Estimating fragment length (mate gap mean=-85.5032, mate gap stddev=28.7537, read length mean=131.223)
[2026-05-28T00:08:00] Filtering read-through fragments with a distance <=10000bp (remaining=2427775)
[2026-05-28T00:08:01] Filtering inconsistently clipped mates (remaining=2387749)
[2026-05-28T00:08:01] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2335426)
[2026-05-28T00:08:03] Filtering fragments with small insert size (remaining=2335030)
[2026-05-28T00:08:04] Filtering alignments with long gaps (remaining=2335030)
[2026-05-28T00:08:05] Filtering fragments with both mates in the same gene (remaining=2334502)
[2026-05-28T00:08:06] Filtering fusions arising from hairpin structures (remaining=2199990)
[2026-05-28T00:08:07] Filtering reads with a mismatch p-value <=0.01 (remaining=1034592)
[2026-05-28T00:08:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=459215)
[2026-05-28T00:08:17] Finding fusions and counting supporting reads (total=384483)
[2026-05-28T00:08:24] Merging adjacent fusion breakpoints (remaining=382234)
[2026-05-28T00:08:25] Filtering multi-mapping fusions by alignment score and read support (remaining=235431)
[2026-05-28T00:08:37] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:08:41] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=234101)
[2026-05-28T00:08:41] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=127772)
[2026-05-28T00:08:42] Filtering fusions with <2 supporting reads (remaining=15420)
[2026-05-28T00:08:42] Filtering fusions with an e-value >=0.3 (remaining=4667)
[2026-05-28T00:08:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4700)
[2026-05-28T00:08:44] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4664)
[2026-05-28T00:08:45] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4664)
[2026-05-28T00:08:45] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3489)
[2026-05-28T00:08:48] Searching for fusions with spliced split reads (remaining=3542)
[2026-05-28T00:08:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=2434)
[2026-05-28T00:08:51] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2416)
[2026-05-28T00:08:51] Searching for fusions with >=4 spliced events (remaining=2821)
[2026-05-28T00:08:52] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1159)
[2026-05-28T00:09:04] Filtering fusions with anchors <=23nt (remaining=980)
[2026-05-28T00:09:05] Filtering end-to-end fusions with low support (remaining=964)
[2026-05-28T00:09:05] Filtering fusions with no coverage around the breakpoints (remaining=940)
[2026-05-28T00:09:05] Indexing gene sequences 
[2026-05-28T00:09:13] Filtering genes with >=30% identity (remaining=416)
[2026-05-28T00:09:16] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=272)
[2026-05-28T00:09:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=196)
[2026-05-28T00:09:25] Searching for additional isoforms (remaining=272)
[2026-05-28T00:09:25] Assigning confidence scores to events 
[2026-05-28T00:09:27] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:09:27] Writing fusions to file 'tih_rna_sample_00461_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-05-28T00:09:29] Writing discarded fusions to file 'tih_rna_sample_00461_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T00:09:44] Freeing resources
[2026-05-28T00:09:52] Done (elapsed time=00:04:53, CPU time=00:04:52, peak memory=8.12gb)