[2026-06-08T08:52:38] Launching Arriba 2.4.0
[2026-06-08T08:52:38] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:50] Reading chimeric alignments from 'tih_rna_sample_00693_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10579253)
[2026-06-08T08:59:38] Marking multi-mapping alignments (marked=6176310)
[2026-06-08T08:59:43] Detecting strandedness (reverse)
[2026-06-08T08:59:43] Assigning strands to alignments 
[2026-06-08T08:59:45] Annotating alignments 
[2026-06-08T09:00:20] Filtering duplicates (remaining=7438225)
[2026-06-08T09:00:28] 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=7192678)
[2026-06-08T09:00:30] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7192678)
[2026-06-08T09:00:33] Filtering viral contigs with expression lower than the top 5 (remaining=7192678)
[2026-06-08T09:00:38] Filtering viral contigs with less than 5% coverage (remaining=7192678)
[2026-06-08T09:00:40] Estimating fragment length (mate gap mean=-86.1708, mate gap stddev=31.1062, read length mean=137.758)
[2026-06-08T09:00:40] Filtering read-through fragments with a distance <=10000bp (remaining=6747459)
[2026-06-08T09:00:42] Filtering inconsistently clipped mates (remaining=6655423)
[2026-06-08T09:00:45] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6501746)
[2026-06-08T09:00:50] Filtering fragments with small insert size (remaining=6501199)
[2026-06-08T09:00:52] Filtering alignments with long gaps (remaining=6501199)
[2026-06-08T09:00:55] Filtering fragments with both mates in the same gene (remaining=6499985)
[2026-06-08T09:00:57] Filtering fusions arising from hairpin structures (remaining=6140589)
[2026-06-08T09:01:00] Filtering reads with a mismatch p-value <=0.01 (remaining=3334137)
[2026-06-08T09:01:16] Filtering reads with low entropy (k-mer content >=60%) (remaining=1292992)
[2026-06-08T09:01:29] Finding fusions and counting supporting reads (total=925614)
[2026-06-08T09:01:47] Merging adjacent fusion breakpoints (remaining=917631)
[2026-06-08T09:01:49] Filtering multi-mapping fusions by alignment score and read support (remaining=615383)
[2026-06-08T09:02:24] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:02:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=611663)
[2026-06-08T09:02:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=347321)
[2026-06-08T09:02:34] Filtering fusions with <2 supporting reads (remaining=48395)
[2026-06-08T09:02:35] Filtering fusions with an e-value >=0.3 (remaining=16097)
[2026-06-08T09:02:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=16160)
[2026-06-08T09:02:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=16011)
[2026-06-08T09:02:41] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=16011)
[2026-06-08T09:02:43] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10451)
[2026-06-08T09:02:48] Searching for fusions with spliced split reads (remaining=10525)
[2026-06-08T09:02:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=5368)
[2026-06-08T09:02:55] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5259)
[2026-06-08T09:02:56] Searching for fusions with >=4 spliced events (remaining=6724)
[2026-06-08T09:02:58] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2827)
[2026-06-08T09:03:13] Filtering fusions with anchors <=23nt (remaining=2276)
[2026-06-08T09:03:14] Filtering end-to-end fusions with low support (remaining=2196)
[2026-06-08T09:03:15] Filtering fusions with no coverage around the breakpoints (remaining=2128)
[2026-06-08T09:03:16] Indexing gene sequences 
[2026-06-08T09:03:23] Filtering genes with >=30% identity (remaining=641)
[2026-06-08T09:03:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=324)
[2026-06-08T09:03:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=217)
[2026-06-08T09:03:36] Searching for additional isoforms (remaining=315)
[2026-06-08T09:03:37] Assigning confidence scores to events 
[2026-06-08T09:03:41] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:03:41] Writing fusions to file 'tih_rna_sample_00693_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:03:44] Writing discarded fusions to file 'tih_rna_sample_00693_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:04:19] Freeing resources
[2026-06-08T09:04:38] Done (elapsed time=00:12:00, CPU time=00:11:58, peak memory=15.2gb)