[2026-06-08T08:46:52] Launching Arriba 2.4.0
[2026-06-08T08:46:52] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:05] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:10] Reading chimeric alignments from 'tih_rna_sample_00097_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10727954)
[2026-06-08T08:55:18] Marking multi-mapping alignments (marked=6949216)
[2026-06-08T08:55:23] Detecting strandedness (reverse)
[2026-06-08T08:55:23] Assigning strands to alignments 
[2026-06-08T08:55:25] Annotating alignments 
[2026-06-08T08:56:04] Filtering duplicates (remaining=4097469)
[2026-06-08T08:56:09] 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=3869589)
[2026-06-08T08:56:12] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3869589)
[2026-06-08T08:56:14] Filtering viral contigs with expression lower than the top 5 (remaining=3869589)
[2026-06-08T08:56:19] Filtering viral contigs with less than 5% coverage (remaining=3869589)
[2026-06-08T08:56:22] Estimating fragment length (mate gap mean=-86.7638, mate gap stddev=26.94, read length mean=126.324)
[2026-06-08T08:56:22] Filtering read-through fragments with a distance <=10000bp (remaining=3585662)
[2026-06-08T08:56:24] Filtering inconsistently clipped mates (remaining=3527385)
[2026-06-08T08:56:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3421511)
[2026-06-08T08:56:30] Filtering fragments with small insert size (remaining=3420826)
[2026-06-08T08:56:32] Filtering alignments with long gaps (remaining=3420826)
[2026-06-08T08:56:35] Filtering fragments with both mates in the same gene (remaining=3420113)
[2026-06-08T08:56:37] Filtering fusions arising from hairpin structures (remaining=3272285)
[2026-06-08T08:56:39] Filtering reads with a mismatch p-value <=0.01 (remaining=1353659)
[2026-06-08T08:56:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=675235)
[2026-06-08T08:56:57] Finding fusions and counting supporting reads (total=540417)
[2026-06-08T08:57:12] Merging adjacent fusion breakpoints (remaining=531984)
[2026-06-08T08:57:13] Filtering multi-mapping fusions by alignment score and read support (remaining=302493)
[2026-06-08T08:57:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=301444)
[2026-06-08T08:57:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=164168)
[2026-06-08T08:57:55] Filtering fusions with <2 supporting reads (remaining=21255)
[2026-06-08T08:57:55] Filtering fusions with an e-value >=0.3 (remaining=5208)
[2026-06-08T08:57:56] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5240)
[2026-06-08T08:57:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5120)
[2026-06-08T08:58:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5120)
[2026-06-08T08:58:01] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4889)
[2026-06-08T08:58:05] Searching for fusions with spliced split reads (remaining=4936)
[2026-06-08T08:58:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=3168)
[2026-06-08T08:58:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3135)
[2026-06-08T08:58:11] Searching for fusions with >=4 spliced events (remaining=3658)
[2026-06-08T08:58:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1632)
[2026-06-08T08:58:25] Filtering fusions with anchors <=23nt (remaining=1398)
[2026-06-08T08:58:26] Filtering end-to-end fusions with low support (remaining=1352)
[2026-06-08T08:58:26] Filtering fusions with no coverage around the breakpoints (remaining=1322)
[2026-06-08T08:58:27] Indexing gene sequences 
[2026-06-08T08:58:31] Filtering genes with >=30% identity (remaining=433)
[2026-06-08T08:58:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=148)
[2026-06-08T08:58:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=134)
[2026-06-08T08:58:36] Searching for additional isoforms (remaining=177)
[2026-06-08T08:58:37] Assigning confidence scores to events 
[2026-06-08T08:58:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:39] Writing fusions to file 'tih_rna_sample_00097_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:58:41] Writing discarded fusions to file 'tih_rna_sample_00097_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:02] Freeing resources
[2026-06-08T08:59:19] Done (elapsed time=00:12:27, CPU time=00:12:25, peak memory=15.2gb)