[2026-06-08T08:28:25] Launching Arriba 2.4.0
[2026-06-08T08:28:25] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:28:35] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:28:39] Reading chimeric alignments from 'tih_rna_sample_00764_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=9885114)
[2026-06-08T08:35:29] Marking multi-mapping alignments (marked=6196699)
[2026-06-08T08:35:35] Detecting strandedness (reverse)
[2026-06-08T08:35:35] Assigning strands to alignments 
[2026-06-08T08:35:38] Annotating alignments 
[2026-06-08T08:36:31] Filtering duplicates (remaining=5904235)
[2026-06-08T08:36:41] 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=5605087)
[2026-06-08T08:36:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5605087)
[2026-06-08T08:36:47] Filtering viral contigs with expression lower than the top 5 (remaining=5605087)
[2026-06-08T08:36:55] Filtering viral contigs with less than 5% coverage (remaining=5605087)
[2026-06-08T08:36:58] Estimating fragment length (mate gap mean=-87.5436, mate gap stddev=27.879, read length mean=130.045)
[2026-06-08T08:36:58] Filtering read-through fragments with a distance <=10000bp (remaining=5306628)
[2026-06-08T08:37:02] Filtering inconsistently clipped mates (remaining=5203489)
[2026-06-08T08:37:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5093807)
[2026-06-08T08:37:11] Filtering fragments with small insert size (remaining=5093184)
[2026-06-08T08:37:14] Filtering alignments with long gaps (remaining=5093184)
[2026-06-08T08:37:17] Filtering fragments with both mates in the same gene (remaining=5092242)
[2026-06-08T08:37:20] Filtering fusions arising from hairpin structures (remaining=4762479)
[2026-06-08T08:37:24] Filtering reads with a mismatch p-value <=0.01 (remaining=2318833)
[2026-06-08T08:37:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=947586)
[2026-06-08T08:37:52] Finding fusions and counting supporting reads (total=628122)
[2026-06-08T08:38:16] Merging adjacent fusion breakpoints (remaining=622562)
[2026-06-08T08:38:19] Filtering multi-mapping fusions by alignment score and read support (remaining=391084)
[2026-06-08T08:39:07] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:39:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=389439)
[2026-06-08T08:39:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=229439)
[2026-06-08T08:39:19] Filtering fusions with <2 supporting reads (remaining=34950)
[2026-06-08T08:39:20] Filtering fusions with an e-value >=0.3 (remaining=8462)
[2026-06-08T08:39:21] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8523)
[2026-06-08T08:39:27] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8450)
[2026-06-08T08:39:28] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8450)
[2026-06-08T08:39:30] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8166)
[2026-06-08T08:39:37] Searching for fusions with spliced split reads (remaining=8291)
[2026-06-08T08:39:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=5122)
[2026-06-08T08:39:47] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5075)
[2026-06-08T08:39:48] Searching for fusions with >=4 spliced events (remaining=5967)
[2026-06-08T08:39:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2039)
[2026-06-08T08:40:10] Filtering fusions with anchors <=23nt (remaining=1694)
[2026-06-08T08:40:11] Filtering end-to-end fusions with low support (remaining=1650)
[2026-06-08T08:40:12] Filtering fusions with no coverage around the breakpoints (remaining=1609)
[2026-06-08T08:40:13] Indexing gene sequences 
[2026-06-08T08:40:22] Filtering genes with >=30% identity (remaining=536)
[2026-06-08T08:40:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=294)
[2026-06-08T08:40:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=258)
[2026-06-08T08:40:34] Searching for additional isoforms (remaining=325)
[2026-06-08T08:40:36] Assigning confidence scores to events 
[2026-06-08T08:40:40] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:40:40] Writing fusions to file 'tih_rna_sample_00764_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:40:44] Writing discarded fusions to file 'tih_rna_sample_00764_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:41:28] Freeing resources
[2026-06-08T08:41:52] Done (elapsed time=00:13:27, CPU time=00:13:25, peak memory=14.5gb)