[2026-06-08T08:47:54] Launching Arriba 2.4.0
[2026-06-08T08:47:54] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:04] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:09] Reading chimeric alignments from 'tih_rna_sample_00146_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=9443503)
[2026-06-08T08:55:14] Marking multi-mapping alignments (marked=5765198)
[2026-06-08T08:55:19] Detecting strandedness (reverse)
[2026-06-08T08:55:19] Assigning strands to alignments 
[2026-06-08T08:55:21] Annotating alignments 
[2026-06-08T08:55:55] Filtering duplicates (remaining=5593634)
[2026-06-08T08:56:02] 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=5357372)
[2026-06-08T08:56:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5357372)
[2026-06-08T08:56:06] Filtering viral contigs with expression lower than the top 5 (remaining=5357372)
[2026-06-08T08:56:11] Filtering viral contigs with less than 5% coverage (remaining=5357372)
[2026-06-08T08:56:13] Estimating fragment length (mate gap mean=-85.9031, mate gap stddev=31.1675, read length mean=136.595)
[2026-06-08T08:56:13] Filtering read-through fragments with a distance <=10000bp (remaining=4988746)
[2026-06-08T08:56:15] Filtering inconsistently clipped mates (remaining=4912577)
[2026-06-08T08:56:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4765205)
[2026-06-08T08:56:22] Filtering fragments with small insert size (remaining=4764523)
[2026-06-08T08:56:24] Filtering alignments with long gaps (remaining=4764522)
[2026-06-08T08:56:27] Filtering fragments with both mates in the same gene (remaining=4763339)
[2026-06-08T08:56:29] Filtering fusions arising from hairpin structures (remaining=4488417)
[2026-06-08T08:56:32] Filtering reads with a mismatch p-value <=0.01 (remaining=2038438)
[2026-06-08T08:56:44] Filtering reads with low entropy (k-mer content >=60%) (remaining=914208)
[2026-06-08T08:56:55] Finding fusions and counting supporting reads (total=685782)
[2026-06-08T08:57:12] Merging adjacent fusion breakpoints (remaining=679761)
[2026-06-08T08:57:13] Filtering multi-mapping fusions by alignment score and read support (remaining=452603)
[2026-06-08T08:57:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=448163)
[2026-06-08T08:57:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=234776)
[2026-06-08T08:57:54] Filtering fusions with <2 supporting reads (remaining=37659)
[2026-06-08T08:57:55] Filtering fusions with an e-value >=0.3 (remaining=14532)
[2026-06-08T08:57:56] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14581)
[2026-06-08T08:57:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14495)
[2026-06-08T08:58:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14495)
[2026-06-08T08:58:01] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7940)
[2026-06-08T08:58:06] Searching for fusions with spliced split reads (remaining=7962)
[2026-06-08T08:58:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=4529)
[2026-06-08T08:58:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4440)
[2026-06-08T08:58:12] Searching for fusions with >=4 spliced events (remaining=5290)
[2026-06-08T08:58:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1986)
[2026-06-08T08:58:28] Filtering fusions with anchors <=23nt (remaining=1562)
[2026-06-08T08:58:29] Filtering end-to-end fusions with low support (remaining=1513)
[2026-06-08T08:58:29] Filtering fusions with no coverage around the breakpoints (remaining=1463)
[2026-06-08T08:58:30] Indexing gene sequences 
[2026-06-08T08:58:35] Filtering genes with >=30% identity (remaining=443)
[2026-06-08T08:58:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=185)
[2026-06-08T08:58:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=176)
[2026-06-08T08:58:44] Searching for additional isoforms (remaining=265)
[2026-06-08T08:58:45] Assigning confidence scores to events 
[2026-06-08T08:58:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:48] Writing fusions to file 'tih_rna_sample_00146_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:58:51] Writing discarded fusions to file 'tih_rna_sample_00146_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:20] Freeing resources
[2026-06-08T08:59:37] Done (elapsed time=00:11:43, CPU time=00:11:41, peak memory=14.1gb)