[2026-06-08T08:40:37] Launching Arriba 2.4.0
[2026-06-08T08:40:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:40:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:50] Reading chimeric alignments from 'tih_rna_sample_00614_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10487786)
[2026-06-08T08:46:24] Marking multi-mapping alignments (marked=6594431)
[2026-06-08T08:46:28] Detecting strandedness (no)
[2026-06-08T08:46:28] Annotating alignments 
[2026-06-08T08:47:03] Filtering duplicates (remaining=5472937)
[2026-06-08T08:47:09] 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=5190384)
[2026-06-08T08:47:10] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5190384)
[2026-06-08T08:47:12] Filtering viral contigs with expression lower than the top 5 (remaining=5190384)
[2026-06-08T08:47:16] Filtering viral contigs with less than 5% coverage (remaining=5190384)
[2026-06-08T08:47:19] Estimating fragment length (mate gap mean=-87.995, mate gap stddev=27.9984, read length mean=129.114)
[2026-06-08T08:47:19] Filtering read-through fragments with a distance <=10000bp (remaining=4929052)
[2026-06-08T08:47:21] Filtering inconsistently clipped mates (remaining=4829998)
[2026-06-08T08:47:22] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4711627)
[2026-06-08T08:47:26] Filtering fragments with small insert size (remaining=4710911)
[2026-06-08T08:47:28] Filtering alignments with long gaps (remaining=4710911)
[2026-06-08T08:47:30] Filtering fragments with both mates in the same gene (remaining=4710047)
[2026-06-08T08:47:32] Filtering fusions arising from hairpin structures (remaining=4395168)
[2026-06-08T08:47:34] Filtering reads with a mismatch p-value <=0.01 (remaining=2070839)
[2026-06-08T08:47:44] Filtering reads with low entropy (k-mer content >=60%) (remaining=735288)
[2026-06-08T08:47:53] Finding fusions and counting supporting reads (total=539173)
[2026-06-08T08:48:05] Merging adjacent fusion breakpoints (remaining=531117)
[2026-06-08T08:48:06] Filtering multi-mapping fusions by alignment score and read support (remaining=335910)
[2026-06-08T08:48:35] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:48:41] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=334675)
[2026-06-08T08:48:41] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=183069)
[2026-06-08T08:48:42] Filtering fusions with <2 supporting reads (remaining=26821)
[2026-06-08T08:48:43] Filtering fusions with an e-value >=0.3 (remaining=6854)
[2026-06-08T08:48:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6903)
[2026-06-08T08:48:47] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6789)
[2026-06-08T08:48:47] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6789)
[2026-06-08T08:48:48] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6376)
[2026-06-08T08:48:53] Searching for fusions with spliced split reads (remaining=6497)
[2026-06-08T08:48:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=4401)
[2026-06-08T08:48:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4341)
[2026-06-08T08:48:59] Searching for fusions with >=4 spliced events (remaining=5033)
[2026-06-08T08:49:00] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1840)
[2026-06-08T08:49:15] Filtering fusions with anchors <=23nt (remaining=1464)
[2026-06-08T08:49:16] Filtering end-to-end fusions with low support (remaining=1408)
[2026-06-08T08:49:16] Filtering fusions with no coverage around the breakpoints (remaining=1364)
[2026-06-08T08:49:17] Indexing gene sequences 
[2026-06-08T08:49:23] Filtering genes with >=30% identity (remaining=546)
[2026-06-08T08:49:26] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=325)
[2026-06-08T08:49:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=262)
[2026-06-08T08:49:33] Searching for additional isoforms (remaining=334)
[2026-06-08T08:49:34] Assigning confidence scores to events 
[2026-06-08T08:49:37] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:49:37] Writing fusions to file 'tih_rna_sample_00614_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:49:39] Writing discarded fusions to file 'tih_rna_sample_00614_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:01] Freeing resources
[2026-06-08T08:50:16] Done (elapsed time=00:09:39, CPU time=00:09:38, peak memory=15gb)