[2026-06-08T08:32:21] Launching Arriba 2.4.0
[2026-06-08T08:32:21] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:35] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:39] Reading chimeric alignments from 'tih_rna_sample_00709_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=15734695)
[2026-06-08T08:40:29] Marking multi-mapping alignments (marked=10739537)
[2026-06-08T08:40:36] Detecting strandedness (no)
[2026-06-08T08:40:36] Annotating alignments 
[2026-06-08T08:41:44] Filtering duplicates (remaining=5352522)
[2026-06-08T08:41:54] 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=4858768)
[2026-06-08T08:41:58] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4858768)
[2026-06-08T08:42:01] Filtering viral contigs with expression lower than the top 5 (remaining=4858768)
[2026-06-08T08:42:08] Filtering viral contigs with less than 5% coverage (remaining=4858768)
[2026-06-08T08:42:12] Estimating fragment length (mate gap mean=-83.6074, mate gap stddev=29.1105, read length mean=120.389)
[2026-06-08T08:42:12] Filtering read-through fragments with a distance <=10000bp (remaining=4693008)
[2026-06-08T08:42:15] Filtering inconsistently clipped mates (remaining=4627740)
[2026-06-08T08:42:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4536707)
[2026-06-08T08:42:24] Filtering fragments with small insert size (remaining=4535301)
[2026-06-08T08:42:27] Filtering alignments with long gaps (remaining=4535301)
[2026-06-08T08:42:30] Filtering fragments with both mates in the same gene (remaining=4534634)
[2026-06-08T08:42:34] Filtering fusions arising from hairpin structures (remaining=4335812)
[2026-06-08T08:42:37] Filtering reads with a mismatch p-value <=0.01 (remaining=1464376)
[2026-06-08T08:42:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=540186)
[2026-06-08T08:43:02] Finding fusions and counting supporting reads (total=446901)
[2026-06-08T08:43:27] Merging adjacent fusion breakpoints (remaining=441497)
[2026-06-08T08:43:29] Filtering multi-mapping fusions by alignment score and read support (remaining=261025)
[2026-06-08T08:44:19] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:44:25] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=260146)
[2026-06-08T08:44:26] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=160441)
[2026-06-08T08:44:27] Filtering fusions with <2 supporting reads (remaining=15901)
[2026-06-08T08:44:27] Filtering fusions with an e-value >=0.3 (remaining=2862)
[2026-06-08T08:44:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2895)
[2026-06-08T08:44:33] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2817)
[2026-06-08T08:44:33] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2817)
[2026-06-08T08:44:34] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2570)
[2026-06-08T08:44:41] Searching for fusions with spliced split reads (remaining=2692)
[2026-06-08T08:44:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=2081)
[2026-06-08T08:44:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2068)
[2026-06-08T08:44:48] Searching for fusions with >=4 spliced events (remaining=2271)
[2026-06-08T08:44:49] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=924)
[2026-06-08T08:45:05] Filtering fusions with anchors <=23nt (remaining=617)
[2026-06-08T08:45:05] Filtering end-to-end fusions with low support (remaining=528)
[2026-06-08T08:45:06] Filtering fusions with no coverage around the breakpoints (remaining=495)
[2026-06-08T08:45:06] Indexing gene sequences 
[2026-06-08T08:45:10] Filtering genes with >=30% identity (remaining=173)
[2026-06-08T08:45:11] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=103)
[2026-06-08T08:45:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=100)
[2026-06-08T08:45:14] Searching for additional isoforms (remaining=114)
[2026-06-08T08:45:15] Assigning confidence scores to events 
[2026-06-08T08:45:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:45:18] Writing fusions to file 'tih_rna_sample_00709_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:45:19] Writing discarded fusions to file 'tih_rna_sample_00709_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:45:45] Freeing resources
[2026-06-08T08:46:10] Done (elapsed time=00:13:49, CPU time=00:13:47, peak memory=20.3gb)