[2026-06-08T08:39:24] Launching Arriba 2.4.0
[2026-06-08T08:39:24] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:32] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:37] Reading chimeric alignments from 'tih_rna_sample_00692_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10737965)
[2026-06-08T08:45:01] Marking multi-mapping alignments (marked=7249252)
[2026-06-08T08:45:06] Detecting strandedness (reverse)
[2026-06-08T08:45:06] Assigning strands to alignments 
[2026-06-08T08:45:08] Annotating alignments 
[2026-06-08T08:45:44] Filtering duplicates (remaining=4387348)
[2026-06-08T08:45:50] 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=4036742)
[2026-06-08T08:45:52] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4036742)
[2026-06-08T08:45:55] Filtering viral contigs with expression lower than the top 5 (remaining=4036742)
[2026-06-08T08:45:59] Filtering viral contigs with less than 5% coverage (remaining=4036742)
[2026-06-08T08:46:02] Estimating fragment length (mate gap mean=-87.1009, mate gap stddev=28.7094, read length mean=125.609)
[2026-06-08T08:46:02] Filtering read-through fragments with a distance <=10000bp (remaining=3845778)
[2026-06-08T08:46:04] Filtering inconsistently clipped mates (remaining=3760162)
[2026-06-08T08:46:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3617174)
[2026-06-08T08:46:10] Filtering fragments with small insert size (remaining=3616479)
[2026-06-08T08:46:12] Filtering alignments with long gaps (remaining=3616479)
[2026-06-08T08:46:15] Filtering fragments with both mates in the same gene (remaining=3615752)
[2026-06-08T08:46:17] Filtering fusions arising from hairpin structures (remaining=3383608)
[2026-06-08T08:46:19] Filtering reads with a mismatch p-value <=0.01 (remaining=1485870)
[2026-06-08T08:46:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=463872)
[2026-06-08T08:46:37] Finding fusions and counting supporting reads (total=380409)
[2026-06-08T08:46:53] Merging adjacent fusion breakpoints (remaining=376276)
[2026-06-08T08:46:54] Filtering multi-mapping fusions by alignment score and read support (remaining=209852)
[2026-06-08T08:47:28] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:47:33] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=208422)
[2026-06-08T08:47:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=117336)
[2026-06-08T08:47:35] Filtering fusions with <2 supporting reads (remaining=13781)
[2026-06-08T08:47:35] Filtering fusions with an e-value >=0.3 (remaining=3675)
[2026-06-08T08:47:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3719)
[2026-06-08T08:47:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3640)
[2026-06-08T08:47:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3640)
[2026-06-08T08:47:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3539)
[2026-06-08T08:47:46] Searching for fusions with spliced split reads (remaining=3597)
[2026-06-08T08:47:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=2582)
[2026-06-08T08:47:51] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2552)
[2026-06-08T08:47:52] Searching for fusions with >=4 spliced events (remaining=2890)
[2026-06-08T08:47:53] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1004)
[2026-06-08T08:48:07] Filtering fusions with anchors <=23nt (remaining=726)
[2026-06-08T08:48:08] Filtering end-to-end fusions with low support (remaining=703)
[2026-06-08T08:48:08] Filtering fusions with no coverage around the breakpoints (remaining=681)
[2026-06-08T08:48:09] Indexing gene sequences 
[2026-06-08T08:48:12] Filtering genes with >=30% identity (remaining=193)
[2026-06-08T08:48:13] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=65)
[2026-06-08T08:48:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=53)
[2026-06-08T08:48:16] Searching for additional isoforms (remaining=76)
[2026-06-08T08:48:17] Assigning confidence scores to events 
[2026-06-08T08:48:19] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:48:19] Writing fusions to file 'tih_rna_sample_00692_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:48:20] Writing discarded fusions to file 'tih_rna_sample_00692_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:48:42] Freeing resources
[2026-06-08T08:48:58] Done (elapsed time=00:09:34, CPU time=00:09:33, peak memory=15.2gb)