[2026-06-08T07:26:27] Launching Arriba 2.4.0
[2026-06-08T07:26:27] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:26:35] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:26:38] Reading chimeric alignments from 'tih_rna_sample_00422_23H5VFLT4_s47.Aligned.sortedByCoord.out.bam' (total=5455775)
[2026-06-08T07:28:50] Marking multi-mapping alignments (marked=4199789)
[2026-06-08T07:28:52] Detecting strandedness (reverse)
[2026-06-08T07:28:52] Assigning strands to alignments 
[2026-06-08T07:28:54] Annotating alignments 
[2026-06-08T07:29:19] Filtering duplicates (remaining=2485223)
[2026-06-08T07:29:23] 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=2221207)
[2026-06-08T07:29:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2221207)
[2026-06-08T07:29:26] Filtering viral contigs with expression lower than the top 5 (remaining=2221207)
[2026-06-08T07:29:28] Filtering viral contigs with less than 5% coverage (remaining=2221207)
[2026-06-08T07:29:29] Estimating fragment length (mate gap mean=-69.9833, mate gap stddev=29.7426, read length mean=103.592)
[2026-06-08T07:29:29] Filtering read-through fragments with a distance <=10000bp (remaining=2145859)
[2026-06-08T07:29:30] Filtering inconsistently clipped mates (remaining=2090636)
[2026-06-08T07:29:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1698856)
[2026-06-08T07:29:34] Filtering fragments with small insert size (remaining=1697491)
[2026-06-08T07:29:35] Filtering alignments with long gaps (remaining=1697491)
[2026-06-08T07:29:37] Filtering fragments with both mates in the same gene (remaining=1696503)
[2026-06-08T07:29:38] Filtering fusions arising from hairpin structures (remaining=1597484)
[2026-06-08T07:29:39] Filtering reads with a mismatch p-value <=0.01 (remaining=388974)
[2026-06-08T07:29:44] Filtering reads with low entropy (k-mer content >=60%) (remaining=242890)
[2026-06-08T07:29:48] Finding fusions and counting supporting reads (total=254508)
[2026-06-08T07:29:58] Merging adjacent fusion breakpoints (remaining=253612)
[2026-06-08T07:29:59] Filtering multi-mapping fusions by alignment score and read support (remaining=102658)
[2026-06-08T07:30:22] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:30:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=101566)
[2026-06-08T07:30:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=81427)
[2026-06-08T07:30:27] Filtering fusions with <2 supporting reads (remaining=2302)
[2026-06-08T07:30:28] Filtering fusions with an e-value >=0.3 (remaining=597)
[2026-06-08T07:30:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=606)
[2026-06-08T07:30:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=509)
[2026-06-08T07:30:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=509)
[2026-06-08T07:30:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=499)
[2026-06-08T07:30:35] Searching for fusions with spliced split reads (remaining=527)
[2026-06-08T07:30:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=443)
[2026-06-08T07:30:39] Filtering read-through fusions with breakpoints near the gene boundary (remaining=438)
[2026-06-08T07:30:39] Searching for fusions with >=4 spliced events (remaining=454)
[2026-06-08T07:30:40] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=106)
[2026-06-08T07:31:00] Filtering fusions with anchors <=23nt (remaining=88)
[2026-06-08T07:31:00] Filtering end-to-end fusions with low support (remaining=83)
[2026-06-08T07:31:01] Filtering fusions with no coverage around the breakpoints (remaining=79)
[2026-06-08T07:31:01] Indexing gene sequences 
[2026-06-08T07:31:03] Filtering genes with >=30% identity (remaining=41)
[2026-06-08T07:31:03] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=20)
[2026-06-08T07:31:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=20)
[2026-06-08T07:31:05] Searching for additional isoforms (remaining=22)
[2026-06-08T07:31:06] Assigning confidence scores to events 
[2026-06-08T07:31:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:31:08] Writing fusions to file 'tih_rna_sample_00422_23H5VFLT4_s47.arriba.fusions.tsv' 
[2026-06-08T07:31:08] Writing discarded fusions to file 'tih_rna_sample_00422_23H5VFLT4_s47.arriba.fusions.discarded.tsv'
[2026-06-08T07:31:29] Freeing resources
[2026-06-08T07:31:43] Done (elapsed time=00:05:16, CPU time=00:05:15, peak memory=9.99gb)