[2026-06-08T08:47:39] Launching Arriba 2.4.0
[2026-06-08T08:47:39] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:52] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:58] Reading chimeric alignments from 'tih_rna_sample_00731_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11560413)
[2026-06-08T08:55:58] Marking multi-mapping alignments (marked=7561356)
[2026-06-08T08:56:03] Detecting strandedness (reverse)
[2026-06-08T08:56:03] Assigning strands to alignments 
[2026-06-08T08:56:05] Annotating alignments 
[2026-06-08T08:56:44] Filtering duplicates (remaining=7242576)
[2026-06-08T08:56:53] 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=6899241)
[2026-06-08T08:56:55] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6899241)
[2026-06-08T08:56:58] Filtering viral contigs with expression lower than the top 5 (remaining=6899241)
[2026-06-08T08:57:03] Filtering viral contigs with less than 5% coverage (remaining=6899241)
[2026-06-08T08:57:06] Estimating fragment length (mate gap mean=-87.3261, mate gap stddev=29.1601, read length mean=134.309)
[2026-06-08T08:57:06] Filtering read-through fragments with a distance <=10000bp (remaining=6575093)
[2026-06-08T08:57:08] Filtering inconsistently clipped mates (remaining=6462377)
[2026-06-08T08:57:11] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6315635)
[2026-06-08T08:57:16] Filtering fragments with small insert size (remaining=6315023)
[2026-06-08T08:57:19] Filtering alignments with long gaps (remaining=6315023)
[2026-06-08T08:57:21] Filtering fragments with both mates in the same gene (remaining=6314089)
[2026-06-08T08:57:24] Filtering fusions arising from hairpin structures (remaining=5907015)
[2026-06-08T08:57:27] Filtering reads with a mismatch p-value <=0.01 (remaining=2909385)
[2026-06-08T08:57:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=947202)
[2026-06-08T08:57:55] Finding fusions and counting supporting reads (total=696111)
[2026-06-08T08:58:14] Merging adjacent fusion breakpoints (remaining=688643)
[2026-06-08T08:58:15] Filtering multi-mapping fusions by alignment score and read support (remaining=417012)
[2026-06-08T08:58:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=414411)
[2026-06-08T08:59:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=242114)
[2026-06-08T08:59:04] Filtering fusions with <2 supporting reads (remaining=31459)
[2026-06-08T08:59:05] Filtering fusions with an e-value >=0.3 (remaining=8989)
[2026-06-08T08:59:06] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9044)
[2026-06-08T08:59:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8989)
[2026-06-08T08:59:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8989)
[2026-06-08T08:59:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7298)
[2026-06-08T08:59:19] Searching for fusions with spliced split reads (remaining=7384)
[2026-06-08T08:59:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=4566)
[2026-06-08T08:59:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4526)
[2026-06-08T08:59:27] Searching for fusions with >=4 spliced events (remaining=5397)
[2026-06-08T08:59:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2088)
[2026-06-08T08:59:44] Filtering fusions with anchors <=23nt (remaining=1646)
[2026-06-08T08:59:45] Filtering end-to-end fusions with low support (remaining=1587)
[2026-06-08T08:59:46] Filtering fusions with no coverage around the breakpoints (remaining=1555)
[2026-06-08T08:59:47] Indexing gene sequences 
[2026-06-08T08:59:52] Filtering genes with >=30% identity (remaining=464)
[2026-06-08T08:59:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=178)
[2026-06-08T08:59:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=158)
[2026-06-08T09:00:00] Searching for additional isoforms (remaining=204)
[2026-06-08T09:00:01] Assigning confidence scores to events 
[2026-06-08T09:00:05] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:05] Writing fusions to file 'tih_rna_sample_00731_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:00:07] Writing discarded fusions to file 'tih_rna_sample_00731_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:41] Freeing resources
[2026-06-08T09:01:01] Done (elapsed time=00:13:22, CPU time=00:13:21, peak memory=16.1gb)