[2026-06-08T08:24:19] Launching Arriba 2.4.0
[2026-06-08T08:24:19] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:24:27] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:24:32] Reading chimeric alignments from 'tih_rna_sample_00643_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11840799)
[2026-06-08T08:29:36] Marking multi-mapping alignments (marked=8398283)
[2026-06-08T08:29:41] Detecting strandedness (reverse)
[2026-06-08T08:29:41] Assigning strands to alignments 
[2026-06-08T08:29:43] Annotating alignments 
[2026-06-08T08:30:21] Filtering duplicates (remaining=4499613)
[2026-06-08T08:30:27] 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=4135618)
[2026-06-08T08:30:29] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4135618)
[2026-06-08T08:30:31] Filtering viral contigs with expression lower than the top 5 (remaining=4135618)
[2026-06-08T08:30:36] Filtering viral contigs with less than 5% coverage (remaining=4135618)
[2026-06-08T08:30:39] Estimating fragment length (mate gap mean=-84.679, mate gap stddev=28.1372, read length mean=120.643)
[2026-06-08T08:30:39] Filtering read-through fragments with a distance <=10000bp (remaining=3925884)
[2026-06-08T08:30:41] Filtering inconsistently clipped mates (remaining=3825057)
[2026-06-08T08:30:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3727681)
[2026-06-08T08:30:47] Filtering fragments with small insert size (remaining=3726760)
[2026-06-08T08:30:49] Filtering alignments with long gaps (remaining=3726760)
[2026-06-08T08:30:52] Filtering fragments with both mates in the same gene (remaining=3725991)
[2026-06-08T08:30:54] Filtering fusions arising from hairpin structures (remaining=3486364)
[2026-06-08T08:30:57] Filtering reads with a mismatch p-value <=0.01 (remaining=1351528)
[2026-06-08T08:31:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=475795)
[2026-06-08T08:31:14] Finding fusions and counting supporting reads (total=394587)
[2026-06-08T08:31:31] Merging adjacent fusion breakpoints (remaining=388397)
[2026-06-08T08:31:32] Filtering multi-mapping fusions by alignment score and read support (remaining=214878)
[2026-06-08T08:32:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:32:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=213981)
[2026-06-08T08:32:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=125837)
[2026-06-08T08:32:16] Filtering fusions with <2 supporting reads (remaining=12560)
[2026-06-08T08:32:17] Filtering fusions with an e-value >=0.3 (remaining=2845)
[2026-06-08T08:32:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2886)
[2026-06-08T08:32:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2833)
[2026-06-08T08:32:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2833)
[2026-06-08T08:32:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2814)
[2026-06-08T08:32:28] Searching for fusions with spliced split reads (remaining=2857)
[2026-06-08T08:32:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=2121)
[2026-06-08T08:32:34] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2103)
[2026-06-08T08:32:34] Searching for fusions with >=4 spliced events (remaining=2361)
[2026-06-08T08:32:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=974)
[2026-06-08T08:32:47] Filtering fusions with anchors <=23nt (remaining=744)
[2026-06-08T08:32:48] Filtering end-to-end fusions with low support (remaining=696)
[2026-06-08T08:32:48] Filtering fusions with no coverage around the breakpoints (remaining=671)
[2026-06-08T08:32:49] Indexing gene sequences 
[2026-06-08T08:32:52] Filtering genes with >=30% identity (remaining=222)
[2026-06-08T08:32:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=97)
[2026-06-08T08:32:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=91)
[2026-06-08T08:32:56] Searching for additional isoforms (remaining=102)
[2026-06-08T08:32:57] Assigning confidence scores to events 
[2026-06-08T08:32:59] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:32:59] Writing fusions to file 'tih_rna_sample_00643_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:33:00] Writing discarded fusions to file 'tih_rna_sample_00643_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:33:22] Freeing resources
[2026-06-08T08:33:40] Done (elapsed time=00:09:21, CPU time=00:09:20, peak memory=16.3gb)