[2026-06-08T08:18:17] Launching Arriba 2.4.0
[2026-06-08T08:18:17] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:18:26] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:18:30] Reading chimeric alignments from 'tih_rna_sample_00766_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=9783466)
[2026-06-08T08:23:04] Marking multi-mapping alignments (marked=6730022)
[2026-06-08T08:23:08] Detecting strandedness (reverse)
[2026-06-08T08:23:08] Assigning strands to alignments 
[2026-06-08T08:23:10] Annotating alignments 
[2026-06-08T08:23:42] Filtering duplicates (remaining=4441833)
[2026-06-08T08:23:47] 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=4153553)
[2026-06-08T08:23:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4153553)
[2026-06-08T08:23:51] Filtering viral contigs with expression lower than the top 5 (remaining=4153553)
[2026-06-08T08:23:55] Filtering viral contigs with less than 5% coverage (remaining=4153553)
[2026-06-08T08:23:57] Estimating fragment length (mate gap mean=-85.5673, mate gap stddev=27.3515, read length mean=123.125)
[2026-06-08T08:23:57] Filtering read-through fragments with a distance <=10000bp (remaining=3960396)
[2026-06-08T08:23:59] Filtering inconsistently clipped mates (remaining=3865794)
[2026-06-08T08:24:01] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3758377)
[2026-06-08T08:24:05] Filtering fragments with small insert size (remaining=3757516)
[2026-06-08T08:24:07] Filtering alignments with long gaps (remaining=3757516)
[2026-06-08T08:24:09] Filtering fragments with both mates in the same gene (remaining=3756748)
[2026-06-08T08:24:12] Filtering fusions arising from hairpin structures (remaining=3511773)
[2026-06-08T08:24:15] Filtering reads with a mismatch p-value <=0.01 (remaining=1456540)
[2026-06-08T08:24:30] Filtering reads with low entropy (k-mer content >=60%) (remaining=497465)
[2026-06-08T08:24:39] Finding fusions and counting supporting reads (total=431295)
[2026-06-08T08:24:54] Merging adjacent fusion breakpoints (remaining=426868)
[2026-06-08T08:24:55] Filtering multi-mapping fusions by alignment score and read support (remaining=229974)
[2026-06-08T08:25:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:25:34] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=228829)
[2026-06-08T08:25:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=139940)
[2026-06-08T08:25:35] Filtering fusions with <2 supporting reads (remaining=11692)
[2026-06-08T08:25:36] Filtering fusions with an e-value >=0.3 (remaining=2937)
[2026-06-08T08:25:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2999)
[2026-06-08T08:25:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2924)
[2026-06-08T08:25:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2924)
[2026-06-08T08:25:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2877)
[2026-06-08T08:25:46] Searching for fusions with spliced split reads (remaining=2939)
[2026-06-08T08:25:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=2059)
[2026-06-08T08:25:51] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2035)
[2026-06-08T08:25:52] Searching for fusions with >=4 spliced events (remaining=2363)
[2026-06-08T08:25:53] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=998)
[2026-06-08T08:26:05] Filtering fusions with anchors <=23nt (remaining=831)
[2026-06-08T08:26:05] Filtering end-to-end fusions with low support (remaining=795)
[2026-06-08T08:26:06] Filtering fusions with no coverage around the breakpoints (remaining=773)
[2026-06-08T08:26:06] Indexing gene sequences 
[2026-06-08T08:26:10] Filtering genes with >=30% identity (remaining=232)
[2026-06-08T08:26:11] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=97)
[2026-06-08T08:26:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=84)
[2026-06-08T08:26:14] Searching for additional isoforms (remaining=103)
[2026-06-08T08:26:15] Assigning confidence scores to events 
[2026-06-08T08:26:17] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:26:18] Writing fusions to file 'tih_rna_sample_00766_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:26:18] Writing discarded fusions to file 'tih_rna_sample_00766_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:26:41] Freeing resources
[2026-06-08T08:26:58] Done (elapsed time=00:08:41, CPU time=00:08:40, peak memory=14.2gb)