[2026-06-08T08:52:34] Launching Arriba 2.4.0
[2026-06-08T08:52:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:54] Reading chimeric alignments from 'tih_rna_sample_00622_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11330545)
[2026-06-08T09:02:33] Marking multi-mapping alignments (marked=6930302)
[2026-06-08T09:02:41] Detecting strandedness (reverse)
[2026-06-08T09:02:41] Assigning strands to alignments 
[2026-06-08T09:02:45] Annotating alignments 
[2026-06-08T09:03:51] Filtering duplicates (remaining=7396936)
[2026-06-08T09:04:02] 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=7149571)
[2026-06-08T09:04:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7149571)
[2026-06-08T09:04:09] Filtering viral contigs with expression lower than the top 5 (remaining=7149571)
[2026-06-08T09:04:17] Filtering viral contigs with less than 5% coverage (remaining=7149571)
[2026-06-08T09:04:21] Estimating fragment length (mate gap mean=-85.0304, mate gap stddev=28.4553, read length mean=130.135)
[2026-06-08T09:04:21] Filtering read-through fragments with a distance <=10000bp (remaining=6664343)
[2026-06-08T09:04:24] Filtering inconsistently clipped mates (remaining=6549909)
[2026-06-08T09:04:28] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6424216)
[2026-06-08T09:04:35] Filtering fragments with small insert size (remaining=6422946)
[2026-06-08T09:04:38] Filtering alignments with long gaps (remaining=6422945)
[2026-06-08T09:04:42] Filtering fragments with both mates in the same gene (remaining=6421724)
[2026-06-08T09:04:46] Filtering fusions arising from hairpin structures (remaining=6051635)
[2026-06-08T09:04:50] Filtering reads with a mismatch p-value <=0.01 (remaining=3029609)
[2026-06-08T09:05:08] Filtering reads with low entropy (k-mer content >=60%) (remaining=1135321)
[2026-06-08T09:05:23] Finding fusions and counting supporting reads (total=850726)
[2026-06-08T09:05:56] Merging adjacent fusion breakpoints (remaining=840900)
[2026-06-08T09:06:00] Filtering multi-mapping fusions by alignment score and read support (remaining=536084)
[2026-06-08T09:07:03] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:07:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=533559)
[2026-06-08T09:07:23] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=285080)
[2026-06-08T09:07:26] Filtering fusions with <2 supporting reads (remaining=40828)
[2026-06-08T09:07:27] Filtering fusions with an e-value >=0.3 (remaining=12018)
[2026-06-08T09:07:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12081)
[2026-06-08T09:07:36] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12012)
[2026-06-08T09:07:37] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12012)
[2026-06-08T09:07:40] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8108)
[2026-06-08T09:07:53] Searching for fusions with spliced split reads (remaining=8239)
[2026-06-08T09:08:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=4907)
[2026-06-08T09:08:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4838)
[2026-06-08T09:08:09] Searching for fusions with >=4 spliced events (remaining=5903)
[2026-06-08T09:08:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2396)
[2026-06-08T09:08:40] Filtering fusions with anchors <=23nt (remaining=2028)
[2026-06-08T09:08:41] Filtering end-to-end fusions with low support (remaining=1978)
[2026-06-08T09:08:43] Filtering fusions with no coverage around the breakpoints (remaining=1938)
[2026-06-08T09:08:44] Indexing gene sequences 
[2026-06-08T09:09:03] Filtering genes with >=30% identity (remaining=561)
[2026-06-08T09:09:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=202)
[2026-06-08T09:09:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=180)
[2026-06-08T09:09:19] Searching for additional isoforms (remaining=227)
[2026-06-08T09:09:22] Assigning confidence scores to events 
[2026-06-08T09:09:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:09:30] Writing fusions to file 'tih_rna_sample_00622_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:09:34] Writing discarded fusions to file 'tih_rna_sample_00622_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:10:35] Freeing resources
[2026-06-08T09:11:12] Done (elapsed time=00:18:38, CPU time=00:18:38, peak memory=15.8gb)