[2026-06-08T08:50:37] Launching Arriba 2.4.0
[2026-06-08T08:50:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:50:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:50:50] Reading chimeric alignments from 'tih_rna_sample_00641_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10738243)
[2026-06-08T08:58:17] Marking multi-mapping alignments (marked=6212784)
[2026-06-08T08:58:21] Detecting strandedness (reverse)
[2026-06-08T08:58:21] Assigning strands to alignments 
[2026-06-08T08:58:24] Annotating alignments 
[2026-06-08T08:59:05] Filtering duplicates (remaining=7472878)
[2026-06-08T08:59:14] 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=7264469)
[2026-06-08T08:59:17] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7264469)
[2026-06-08T08:59:19] Filtering viral contigs with expression lower than the top 5 (remaining=7264469)
[2026-06-08T08:59:25] Filtering viral contigs with less than 5% coverage (remaining=7264469)
[2026-06-08T08:59:28] Estimating fragment length (mate gap mean=-84.7332, mate gap stddev=30.5782, read length mean=136.341)
[2026-06-08T08:59:28] Filtering read-through fragments with a distance <=10000bp (remaining=6770022)
[2026-06-08T08:59:31] Filtering inconsistently clipped mates (remaining=6674559)
[2026-06-08T08:59:34] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6533279)
[2026-06-08T08:59:39] Filtering fragments with small insert size (remaining=6532420)
[2026-06-08T08:59:41] Filtering alignments with long gaps (remaining=6532420)
[2026-06-08T08:59:43] Filtering fragments with both mates in the same gene (remaining=6531299)
[2026-06-08T08:59:46] Filtering fusions arising from hairpin structures (remaining=6171178)
[2026-06-08T08:59:49] Filtering reads with a mismatch p-value <=0.01 (remaining=3333735)
[2026-06-08T09:00:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=1307428)
[2026-06-08T09:00:19] Finding fusions and counting supporting reads (total=949899)
[2026-06-08T09:00:49] Merging adjacent fusion breakpoints (remaining=941247)
[2026-06-08T09:00:52] Filtering multi-mapping fusions by alignment score and read support (remaining=635415)
[2026-06-08T09:01:35] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:01:44] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=632058)
[2026-06-08T09:01:45] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=338178)
[2026-06-08T09:01:47] Filtering fusions with <2 supporting reads (remaining=53722)
[2026-06-08T09:01:48] Filtering fusions with an e-value >=0.3 (remaining=21017)
[2026-06-08T09:01:49] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=21072)
[2026-06-08T09:01:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=20998)
[2026-06-08T09:01:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=20998)
[2026-06-08T09:01:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9830)
[2026-06-08T09:02:03] Searching for fusions with spliced split reads (remaining=9894)
[2026-06-08T09:02:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=5260)
[2026-06-08T09:02:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5179)
[2026-06-08T09:02:11] Searching for fusions with >=4 spliced events (remaining=6510)
[2026-06-08T09:02:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2561)
[2026-06-08T09:02:27] Filtering fusions with anchors <=23nt (remaining=2155)
[2026-06-08T09:02:28] Filtering end-to-end fusions with low support (remaining=2101)
[2026-06-08T09:02:29] Filtering fusions with no coverage around the breakpoints (remaining=2054)
[2026-06-08T09:02:30] Indexing gene sequences 
[2026-06-08T09:02:37] Filtering genes with >=30% identity (remaining=594)
[2026-06-08T09:02:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=240)
[2026-06-08T09:02:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=189)
[2026-06-08T09:02:51] Searching for additional isoforms (remaining=261)
[2026-06-08T09:02:53] Assigning confidence scores to events 
[2026-06-08T09:02:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:02:57] Writing fusions to file 'tih_rna_sample_00641_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:03:00] Writing discarded fusions to file 'tih_rna_sample_00641_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:03:38] Freeing resources
[2026-06-08T09:03:59] Done (elapsed time=00:13:22, CPU time=00:13:21, peak memory=15.3gb)