[2026-06-08T08:23:22] Launching Arriba 2.4.0
[2026-06-08T08:23:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:23:35] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:23:39] Reading chimeric alignments from 'tih_rna_sample_00583_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=12906810)
[2026-06-08T08:29:22] Marking multi-mapping alignments (marked=8962820)
[2026-06-08T08:29:27] Detecting strandedness (reverse)
[2026-06-08T08:29:27] Assigning strands to alignments 
[2026-06-08T08:29:29] Annotating alignments 
[2026-06-08T08:30:07] Filtering duplicates (remaining=6074282)
[2026-06-08T08:30:14] 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=5559095)
[2026-06-08T08:30:17] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5559095)
[2026-06-08T08:30:20] Filtering viral contigs with expression lower than the top 5 (remaining=5559095)
[2026-06-08T08:30:25] Filtering viral contigs with less than 5% coverage (remaining=5559095)
[2026-06-08T08:30:28] Estimating fragment length (mate gap mean=-88.3604, mate gap stddev=28.6331, read length mean=127.266)
[2026-06-08T08:30:28] Filtering read-through fragments with a distance <=10000bp (remaining=5361748)
[2026-06-08T08:30:31] Filtering inconsistently clipped mates (remaining=5280709)
[2026-06-08T08:30:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5160169)
[2026-06-08T08:30:38] Filtering fragments with small insert size (remaining=5159281)
[2026-06-08T08:30:40] Filtering alignments with long gaps (remaining=5159281)
[2026-06-08T08:30:42] Filtering fragments with both mates in the same gene (remaining=5158464)
[2026-06-08T08:30:45] Filtering fusions arising from hairpin structures (remaining=4875935)
[2026-06-08T08:30:48] Filtering reads with a mismatch p-value <=0.01 (remaining=1837708)
[2026-06-08T08:31:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=663009)
[2026-06-08T08:31:11] Finding fusions and counting supporting reads (total=537489)
[2026-06-08T08:31:29] Merging adjacent fusion breakpoints (remaining=531042)
[2026-06-08T08:31:31] Filtering multi-mapping fusions by alignment score and read support (remaining=313696)
[2026-06-08T08:32:06] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:32:12] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=312102)
[2026-06-08T08:32:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=196636)
[2026-06-08T08:32:13] Filtering fusions with <2 supporting reads (remaining=21276)
[2026-06-08T08:32:14] Filtering fusions with an e-value >=0.3 (remaining=5126)
[2026-06-08T08:32:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5165)
[2026-06-08T08:32:18] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5034)
[2026-06-08T08:32:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5034)
[2026-06-08T08:32:20] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4439)
[2026-06-08T08:32:25] Searching for fusions with spliced split reads (remaining=4495)
[2026-06-08T08:32:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=3348)
[2026-06-08T08:32:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3314)
[2026-06-08T08:32:32] Searching for fusions with >=4 spliced events (remaining=3751)
[2026-06-08T08:32:33] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1522)
[2026-06-08T08:32:47] Filtering fusions with anchors <=23nt (remaining=1087)
[2026-06-08T08:32:48] Filtering end-to-end fusions with low support (remaining=988)
[2026-06-08T08:32:48] Filtering fusions with no coverage around the breakpoints (remaining=951)
[2026-06-08T08:32:49] Indexing gene sequences 
[2026-06-08T08:32:54] Filtering genes with >=30% identity (remaining=363)
[2026-06-08T08:32:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=199)
[2026-06-08T08:32:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=176)
[2026-06-08T08:32:59] Searching for additional isoforms (remaining=203)
[2026-06-08T08:33:00] Assigning confidence scores to events 
[2026-06-08T08:33:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:33:04] Writing fusions to file 'tih_rna_sample_00583_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:33:05] Writing discarded fusions to file 'tih_rna_sample_00583_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:33:33] Freeing resources
[2026-06-08T08:33:52] Done (elapsed time=00:10:30, CPU time=00:10:29, peak memory=17.8gb)