[2026-06-08T08:39:23] Launching Arriba 2.4.0
[2026-06-08T08:39:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:35] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:39] Reading chimeric alignments from 'tih_rna_sample_00660_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=12230629)
[2026-06-08T08:45:22] Marking multi-mapping alignments (marked=8120772)
[2026-06-08T08:45:26] Detecting strandedness (reverse)
[2026-06-08T08:45:26] Assigning strands to alignments 
[2026-06-08T08:45:28] Annotating alignments 
[2026-06-08T08:46:03] Filtering duplicates (remaining=5967563)
[2026-06-08T08:46:10] 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=5578238)
[2026-06-08T08:46:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5578238)
[2026-06-08T08:46:15] Filtering viral contigs with expression lower than the top 5 (remaining=5578238)
[2026-06-08T08:46:20] Filtering viral contigs with less than 5% coverage (remaining=5578238)
[2026-06-08T08:46:22] Estimating fragment length (mate gap mean=-88.6595, mate gap stddev=27.2481, read length mean=126.669)
[2026-06-08T08:46:22] Filtering read-through fragments with a distance <=10000bp (remaining=5267435)
[2026-06-08T08:46:24] Filtering inconsistently clipped mates (remaining=5194377)
[2026-06-08T08:46:27] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5082873)
[2026-06-08T08:46:31] Filtering fragments with small insert size (remaining=5081941)
[2026-06-08T08:46:33] Filtering alignments with long gaps (remaining=5081941)
[2026-06-08T08:46:35] Filtering fragments with both mates in the same gene (remaining=5081066)
[2026-06-08T08:46:37] Filtering fusions arising from hairpin structures (remaining=4855084)
[2026-06-08T08:46:40] Filtering reads with a mismatch p-value <=0.01 (remaining=1970733)
[2026-06-08T08:46:52] Filtering reads with low entropy (k-mer content >=60%) (remaining=806059)
[2026-06-08T08:47:01] Finding fusions and counting supporting reads (total=643354)
[2026-06-08T08:47:18] Merging adjacent fusion breakpoints (remaining=636757)
[2026-06-08T08:47:20] Filtering multi-mapping fusions by alignment score and read support (remaining=370145)
[2026-06-08T08:47:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:48:00] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=368928)
[2026-06-08T08:48:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=232062)
[2026-06-08T08:48:01] Filtering fusions with <2 supporting reads (remaining=25006)
[2026-06-08T08:48:02] Filtering fusions with an e-value >=0.3 (remaining=5374)
[2026-06-08T08:48:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5413)
[2026-06-08T08:48:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5329)
[2026-06-08T08:48:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5329)
[2026-06-08T08:48:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5046)
[2026-06-08T08:48:13] Searching for fusions with spliced split reads (remaining=5110)
[2026-06-08T08:48:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=3583)
[2026-06-08T08:48:19] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3548)
[2026-06-08T08:48:20] Searching for fusions with >=4 spliced events (remaining=4139)
[2026-06-08T08:48:21] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1698)
[2026-06-08T08:48:35] Filtering fusions with anchors <=23nt (remaining=1325)
[2026-06-08T08:48:35] Filtering end-to-end fusions with low support (remaining=1246)
[2026-06-08T08:48:36] Filtering fusions with no coverage around the breakpoints (remaining=1202)
[2026-06-08T08:48:36] Indexing gene sequences 
[2026-06-08T08:48:42] Filtering genes with >=30% identity (remaining=347)
[2026-06-08T08:48:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=160)
[2026-06-08T08:48:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=156)
[2026-06-08T08:48:47] Searching for additional isoforms (remaining=179)
[2026-06-08T08:48:48] Assigning confidence scores to events 
[2026-06-08T08:48:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:48:52] Writing fusions to file 'tih_rna_sample_00660_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:48:53] Writing discarded fusions to file 'tih_rna_sample_00660_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:49:19] Freeing resources
[2026-06-08T08:49:38] Done (elapsed time=00:10:15, CPU time=00:10:13, peak memory=17gb)