[2026-06-08T08:19:39] Launching Arriba 2.4.0
[2026-06-08T08:19:39] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:19:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:19:53] Reading chimeric alignments from 'tih_rna_sample_00419_23H5VFLT4_s44.Aligned.sortedByCoord.out.bam' (total=9565661)
[2026-06-08T08:26:44] Marking multi-mapping alignments (marked=6321852)
[2026-06-08T08:26:48] Detecting strandedness (reverse)
[2026-06-08T08:26:48] Assigning strands to alignments 
[2026-06-08T08:26:50] Annotating alignments 
[2026-06-08T08:27:25] Filtering duplicates (remaining=6449763)
[2026-06-08T08:27:32] 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=6015191)
[2026-06-08T08:27:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6015191)
[2026-06-08T08:27:36] Filtering viral contigs with expression lower than the top 5 (remaining=6015191)
[2026-06-08T08:27:41] Filtering viral contigs with less than 5% coverage (remaining=6015191)
[2026-06-08T08:27:43] Estimating fragment length (mate gap mean=-84.6105, mate gap stddev=30.4284, read length mean=130.004)
[2026-06-08T08:27:44] Filtering read-through fragments with a distance <=10000bp (remaining=5637866)
[2026-06-08T08:27:45] Filtering inconsistently clipped mates (remaining=5520113)
[2026-06-08T08:27:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5156242)
[2026-06-08T08:27:53] Filtering fragments with small insert size (remaining=5155196)
[2026-06-08T08:27:54] Filtering alignments with long gaps (remaining=5155194)
[2026-06-08T08:27:57] Filtering fragments with both mates in the same gene (remaining=5153775)
[2026-06-08T08:27:59] Filtering fusions arising from hairpin structures (remaining=4726944)
[2026-06-08T08:28:01] Filtering reads with a mismatch p-value <=0.01 (remaining=2084664)
[2026-06-08T08:28:15] Filtering reads with low entropy (k-mer content >=60%) (remaining=1215727)
[2026-06-08T08:28:25] Finding fusions and counting supporting reads (total=1003290)
[2026-06-08T08:28:43] Merging adjacent fusion breakpoints (remaining=997185)
[2026-06-08T08:28:45] Filtering multi-mapping fusions by alignment score and read support (remaining=598064)
[2026-06-08T08:29:19] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:29:27] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=594980)
[2026-06-08T08:29:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=386976)
[2026-06-08T08:29:29] Filtering fusions with <2 supporting reads (remaining=33260)
[2026-06-08T08:29:29] Filtering fusions with an e-value >=0.3 (remaining=8117)
[2026-06-08T08:29:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8174)
[2026-06-08T08:29:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7975)
[2026-06-08T08:29:34] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7975)
[2026-06-08T08:29:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6253)
[2026-06-08T08:29:41] Searching for fusions with spliced split reads (remaining=6267)
[2026-06-08T08:29:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=3931)
[2026-06-08T08:29:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3905)
[2026-06-08T08:29:49] Searching for fusions with >=4 spliced events (remaining=4827)
[2026-06-08T08:29:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1979)
[2026-06-08T08:30:03] Filtering fusions with anchors <=23nt (remaining=1566)
[2026-06-08T08:30:04] Filtering end-to-end fusions with low support (remaining=1532)
[2026-06-08T08:30:04] Filtering fusions with no coverage around the breakpoints (remaining=1515)
[2026-06-08T08:30:05] Indexing gene sequences 
[2026-06-08T08:30:10] Filtering genes with >=30% identity (remaining=427)
[2026-06-08T08:30:13] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=208)
[2026-06-08T08:30:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=173)
[2026-06-08T08:30:17] Searching for additional isoforms (remaining=243)
[2026-06-08T08:30:19] Assigning confidence scores to events 
[2026-06-08T08:30:23] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:30:23] Writing fusions to file 'tih_rna_sample_00419_23H5VFLT4_s44.arriba.fusions.tsv' 
[2026-06-08T08:30:25] Writing discarded fusions to file 'tih_rna_sample_00419_23H5VFLT4_s44.arriba.fusions.discarded.tsv'
[2026-06-08T08:31:00] Freeing resources
[2026-06-08T08:31:18] Done (elapsed time=00:11:39, CPU time=00:11:38, peak memory=14.7gb)