[2026-06-08T08:39:34] Launching Arriba 2.4.0
[2026-06-08T08:39:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:51] Reading chimeric alignments from 'tih_rna_sample_00581_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=14644154)
[2026-06-08T08:46:43] Marking multi-mapping alignments (marked=10171925)
[2026-06-08T08:46:49] Detecting strandedness (reverse)
[2026-06-08T08:46:49] Assigning strands to alignments 
[2026-06-08T08:46:52] Annotating alignments 
[2026-06-08T08:47:36] Filtering duplicates (remaining=5851770)
[2026-06-08T08:47:43] 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=5356391)
[2026-06-08T08:47:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5356391)
[2026-06-08T08:47:48] Filtering viral contigs with expression lower than the top 5 (remaining=5356391)
[2026-06-08T08:47:54] Filtering viral contigs with less than 5% coverage (remaining=5356391)
[2026-06-08T08:47:57] Estimating fragment length (mate gap mean=-86.8233, mate gap stddev=27.8591, read length mean=124.206)
[2026-06-08T08:47:57] Filtering read-through fragments with a distance <=10000bp (remaining=5141337)
[2026-06-08T08:47:59] Filtering inconsistently clipped mates (remaining=5051906)
[2026-06-08T08:48:02] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4936919)
[2026-06-08T08:48:06] Filtering fragments with small insert size (remaining=4935962)
[2026-06-08T08:48:09] Filtering alignments with long gaps (remaining=4935960)
[2026-06-08T08:48:12] Filtering fragments with both mates in the same gene (remaining=4935117)
[2026-06-08T08:48:15] Filtering fusions arising from hairpin structures (remaining=4669185)
[2026-06-08T08:48:18] Filtering reads with a mismatch p-value <=0.01 (remaining=1858428)
[2026-06-08T08:48:30] Filtering reads with low entropy (k-mer content >=60%) (remaining=580393)
[2026-06-08T08:48:40] Finding fusions and counting supporting reads (total=480065)
[2026-06-08T08:48:59] Merging adjacent fusion breakpoints (remaining=470156)
[2026-06-08T08:49:00] Filtering multi-mapping fusions by alignment score and read support (remaining=272142)
[2026-06-08T08:49:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=270755)
[2026-06-08T08:49:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=160901)
[2026-06-08T08:49:48] Filtering fusions with <2 supporting reads (remaining=16821)
[2026-06-08T08:49:49] Filtering fusions with an e-value >=0.3 (remaining=4022)
[2026-06-08T08:49:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4061)
[2026-06-08T08:49:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3917)
[2026-06-08T08:49:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3917)
[2026-06-08T08:49:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3775)
[2026-06-08T08:50:02] Searching for fusions with spliced split reads (remaining=3831)
[2026-06-08T08:50:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=2735)
[2026-06-08T08:50:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2708)
[2026-06-08T08:50:09] Searching for fusions with >=4 spliced events (remaining=3154)
[2026-06-08T08:50:11] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1464)
[2026-06-08T08:50:26] Filtering fusions with anchors <=23nt (remaining=1059)
[2026-06-08T08:50:27] Filtering end-to-end fusions with low support (remaining=993)
[2026-06-08T08:50:28] Filtering fusions with no coverage around the breakpoints (remaining=955)
[2026-06-08T08:50:28] Indexing gene sequences 
[2026-06-08T08:50:32] Filtering genes with >=30% identity (remaining=309)
[2026-06-08T08:50:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=125)
[2026-06-08T08:50:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=102)
[2026-06-08T08:50:36] Searching for additional isoforms (remaining=120)
[2026-06-08T08:50:37] Assigning confidence scores to events 
[2026-06-08T08:50:40] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:50:40] Writing fusions to file 'tih_rna_sample_00581_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:50:41] Writing discarded fusions to file 'tih_rna_sample_00581_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:51:05] Freeing resources
[2026-06-08T08:51:27] Done (elapsed time=00:11:53, CPU time=00:11:51, peak memory=19.2gb)