[2026-06-08T08:15:39] Launching Arriba 2.4.0
[2026-06-08T08:15:39] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:15:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:15:58] Reading chimeric alignments from 'tih_rna_sample_00403_23H5VFLT4_s29.Aligned.sortedByCoord.out.bam' (total=11104720)
[2026-06-08T08:23:13] Marking multi-mapping alignments (marked=7183227)
[2026-06-08T08:23:17] Detecting strandedness (reverse)
[2026-06-08T08:23:17] Assigning strands to alignments 
[2026-06-08T08:23:19] Annotating alignments 
[2026-06-08T08:23:54] Filtering duplicates (remaining=6647525)
[2026-06-08T08:24:00] 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=6190088)
[2026-06-08T08:24:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6190088)
[2026-06-08T08:24:04] Filtering viral contigs with expression lower than the top 5 (remaining=6190088)
[2026-06-08T08:24:08] Filtering viral contigs with less than 5% coverage (remaining=6190088)
[2026-06-08T08:24:11] Estimating fragment length (mate gap mean=-86.017, mate gap stddev=29.2756, read length mean=125.587)
[2026-06-08T08:24:11] Filtering read-through fragments with a distance <=10000bp (remaining=5742987)
[2026-06-08T08:24:13] Filtering inconsistently clipped mates (remaining=5613379)
[2026-06-08T08:24:15] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5140800)
[2026-06-08T08:24:20] Filtering fragments with small insert size (remaining=5139322)
[2026-06-08T08:24:22] Filtering alignments with long gaps (remaining=5139322)
[2026-06-08T08:24:24] Filtering fragments with both mates in the same gene (remaining=5137774)
[2026-06-08T08:24:26] Filtering fusions arising from hairpin structures (remaining=4698869)
[2026-06-08T08:24:28] Filtering reads with a mismatch p-value <=0.01 (remaining=1873025)
[2026-06-08T08:24:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=1253593)
[2026-06-08T08:24:50] Finding fusions and counting supporting reads (total=1039240)
[2026-06-08T08:25:07] Merging adjacent fusion breakpoints (remaining=1030775)
[2026-06-08T08:25:09] Filtering multi-mapping fusions by alignment score and read support (remaining=605192)
[2026-06-08T08:25:39] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:25:46] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=603063)
[2026-06-08T08:25:47] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=381609)
[2026-06-08T08:25:48] Filtering fusions with <2 supporting reads (remaining=33775)
[2026-06-08T08:25:49] Filtering fusions with an e-value >=0.3 (remaining=6835)
[2026-06-08T08:25:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6892)
[2026-06-08T08:25:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6684)
[2026-06-08T08:25:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6684)
[2026-06-08T08:25:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6371)
[2026-06-08T08:26:01] Searching for fusions with spliced split reads (remaining=6485)
[2026-06-08T08:26:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=4406)
[2026-06-08T08:26:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4346)
[2026-06-08T08:26:08] Searching for fusions with >=4 spliced events (remaining=5330)
[2026-06-08T08:26:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1962)
[2026-06-08T08:26:23] Filtering fusions with anchors <=23nt (remaining=1622)
[2026-06-08T08:26:24] Filtering end-to-end fusions with low support (remaining=1587)
[2026-06-08T08:26:25] Filtering fusions with no coverage around the breakpoints (remaining=1570)
[2026-06-08T08:26:25] Indexing gene sequences 
[2026-06-08T08:26:31] Filtering genes with >=30% identity (remaining=428)
[2026-06-08T08:26:34] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=173)
[2026-06-08T08:26:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=163)
[2026-06-08T08:26:38] Searching for additional isoforms (remaining=185)
[2026-06-08T08:26:40] Assigning confidence scores to events 
[2026-06-08T08:26:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:26:44] Writing fusions to file 'tih_rna_sample_00403_23H5VFLT4_s29.arriba.fusions.tsv' 
[2026-06-08T08:26:45] Writing discarded fusions to file 'tih_rna_sample_00403_23H5VFLT4_s29.arriba.fusions.discarded.tsv'
[2026-06-08T08:27:18] Freeing resources
[2026-06-08T08:27:36] Done (elapsed time=00:11:57, CPU time=00:11:56, peak memory=16.5gb)