[2026-06-08T08:46:37] Launching Arriba 2.4.0
[2026-06-08T08:46:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:46:56] Reading chimeric alignments from 'tih_rna_sample_00612_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11518362)
[2026-06-08T08:54:54] Marking multi-mapping alignments (marked=7359616)
[2026-06-08T08:54:59] Detecting strandedness (reverse)
[2026-06-08T08:54:59] Assigning strands to alignments 
[2026-06-08T08:55:02] Annotating alignments 
[2026-06-08T08:55:39] Filtering duplicates (remaining=7172211)
[2026-06-08T08:55:48] 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=6869947)
[2026-06-08T08:55:50] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6869947)
[2026-06-08T08:55:53] Filtering viral contigs with expression lower than the top 5 (remaining=6869947)
[2026-06-08T08:55:58] Filtering viral contigs with less than 5% coverage (remaining=6869947)
[2026-06-08T08:56:01] Estimating fragment length (mate gap mean=-84.545, mate gap stddev=29.5937, read length mean=133.091)
[2026-06-08T08:56:01] Filtering read-through fragments with a distance <=10000bp (remaining=6499517)
[2026-06-08T08:56:04] Filtering inconsistently clipped mates (remaining=6401826)
[2026-06-08T08:56:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6257233)
[2026-06-08T08:56:11] Filtering fragments with small insert size (remaining=6256389)
[2026-06-08T08:56:14] Filtering alignments with long gaps (remaining=6256389)
[2026-06-08T08:56:16] Filtering fragments with both mates in the same gene (remaining=6255413)
[2026-06-08T08:56:19] Filtering fusions arising from hairpin structures (remaining=5914410)
[2026-06-08T08:56:22] Filtering reads with a mismatch p-value <=0.01 (remaining=2986389)
[2026-06-08T08:56:37] Filtering reads with low entropy (k-mer content >=60%) (remaining=937341)
[2026-06-08T08:56:49] Finding fusions and counting supporting reads (total=747578)
[2026-06-08T08:57:08] Merging adjacent fusion breakpoints (remaining=739002)
[2026-06-08T08:57:10] Filtering multi-mapping fusions by alignment score and read support (remaining=469428)
[2026-06-08T08:57:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:57] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=466887)
[2026-06-08T08:57:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=248135)
[2026-06-08T08:58:00] Filtering fusions with <2 supporting reads (remaining=31545)
[2026-06-08T08:58:02] Filtering fusions with an e-value >=0.3 (remaining=9573)
[2026-06-08T08:58:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9627)
[2026-06-08T08:58:09] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9531)
[2026-06-08T08:58:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9531)
[2026-06-08T08:58:12] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7106)
[2026-06-08T08:58:19] Searching for fusions with spliced split reads (remaining=7256)
[2026-06-08T08:58:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=4145)
[2026-06-08T08:58:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4107)
[2026-06-08T08:58:27] Searching for fusions with >=4 spliced events (remaining=5052)
[2026-06-08T08:58:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2121)
[2026-06-08T08:58:44] Filtering fusions with anchors <=23nt (remaining=1750)
[2026-06-08T08:58:44] Filtering end-to-end fusions with low support (remaining=1703)
[2026-06-08T08:58:45] Filtering fusions with no coverage around the breakpoints (remaining=1664)
[2026-06-08T08:58:46] Indexing gene sequences 
[2026-06-08T08:58:52] Filtering genes with >=30% identity (remaining=465)
[2026-06-08T08:58:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=158)
[2026-06-08T08:58:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=136)
[2026-06-08T08:58:59] Searching for additional isoforms (remaining=221)
[2026-06-08T08:59:01] Assigning confidence scores to events 
[2026-06-08T08:59:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:05] Writing fusions to file 'tih_rna_sample_00612_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:07] Writing discarded fusions to file 'tih_rna_sample_00612_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:41] Freeing resources
[2026-06-08T09:00:01] Done (elapsed time=00:13:24, CPU time=00:13:22, peak memory=15.9gb)