[2026-06-08T08:54:35] Launching Arriba 2.4.0
[2026-06-08T08:54:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:54:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:54:48] Reading chimeric alignments from 'tih_rna_sample_00676_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11557061)
[2026-06-08T09:01:43] Marking multi-mapping alignments (marked=7117064)
[2026-06-08T09:01:47] Detecting strandedness (reverse)
[2026-06-08T09:01:47] Assigning strands to alignments 
[2026-06-08T09:01:49] Annotating alignments 
[2026-06-08T09:02:26] Filtering duplicates (remaining=7731330)
[2026-06-08T09:02:34] 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=7452057)
[2026-06-08T09:02:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7452057)
[2026-06-08T09:02:39] Filtering viral contigs with expression lower than the top 5 (remaining=7452057)
[2026-06-08T09:02:44] Filtering viral contigs with less than 5% coverage (remaining=7452057)
[2026-06-08T09:02:47] Estimating fragment length (mate gap mean=-85.5475, mate gap stddev=30.1965, read length mean=136.684)
[2026-06-08T09:02:47] Filtering read-through fragments with a distance <=10000bp (remaining=6989560)
[2026-06-08T09:02:49] Filtering inconsistently clipped mates (remaining=6893553)
[2026-06-08T09:02:51] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6743925)
[2026-06-08T09:02:56] Filtering fragments with small insert size (remaining=6743296)
[2026-06-08T09:02:59] Filtering alignments with long gaps (remaining=6743296)
[2026-06-08T09:03:01] Filtering fragments with both mates in the same gene (remaining=6742074)
[2026-06-08T09:03:03] Filtering fusions arising from hairpin structures (remaining=6380242)
[2026-06-08T09:03:06] Filtering reads with a mismatch p-value <=0.01 (remaining=3330968)
[2026-06-08T09:03:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=1179034)
[2026-06-08T09:03:36] Finding fusions and counting supporting reads (total=876056)
[2026-06-08T09:03:54] Merging adjacent fusion breakpoints (remaining=867888)
[2026-06-08T09:03:56] Filtering multi-mapping fusions by alignment score and read support (remaining=553670)
[2026-06-08T09:04:34] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:04:42] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=550697)
[2026-06-08T09:04:43] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=306300)
[2026-06-08T09:04:45] Filtering fusions with <2 supporting reads (remaining=41916)
[2026-06-08T09:04:46] Filtering fusions with an e-value >=0.3 (remaining=12594)
[2026-06-08T09:04:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12649)
[2026-06-08T09:04:51] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12544)
[2026-06-08T09:04:52] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12544)
[2026-06-08T09:04:54] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9802)
[2026-06-08T09:04:59] Searching for fusions with spliced split reads (remaining=9824)
[2026-06-08T09:05:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=5125)
[2026-06-08T09:05:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5095)
[2026-06-08T09:05:08] Searching for fusions with >=4 spliced events (remaining=6495)
[2026-06-08T09:05:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2706)
[2026-06-08T09:05:24] Filtering fusions with anchors <=23nt (remaining=2239)
[2026-06-08T09:05:25] Filtering end-to-end fusions with low support (remaining=2182)
[2026-06-08T09:05:26] Filtering fusions with no coverage around the breakpoints (remaining=2135)
[2026-06-08T09:05:27] Indexing gene sequences 
[2026-06-08T09:05:33] Filtering genes with >=30% identity (remaining=704)
[2026-06-08T09:05:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=384)
[2026-06-08T09:05:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=213)
[2026-06-08T09:05:50] Searching for additional isoforms (remaining=340)
[2026-06-08T09:05:51] Assigning confidence scores to events 
[2026-06-08T09:05:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:05:55] Writing fusions to file 'tih_rna_sample_00676_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:05:59] Writing discarded fusions to file 'tih_rna_sample_00676_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:06:33] Freeing resources
[2026-06-08T09:06:54] Done (elapsed time=00:12:19, CPU time=00:12:18, peak memory=16.1gb)