[2026-05-28T00:03:54] Launching Arriba 2.4.0
[2026-05-28T00:03:54] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:04:02] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:04:06] Reading chimeric alignments from 'tih_rna_sample_00096_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3278262)
[2026-05-28T00:06:19] Marking multi-mapping alignments (marked=2097524)
[2026-05-28T00:06:20] Detecting strandedness (reverse)
[2026-05-28T00:06:20] Assigning strands to alignments 
[2026-05-28T00:06:21] Annotating alignments 
[2026-05-28T00:06:33] Filtering duplicates (remaining=2159192)
[2026-05-28T00:06:35] 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=2047305)
[2026-05-28T00:06:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2047305)
[2026-05-28T00:06:36] Filtering viral contigs with expression lower than the top 5 (remaining=2047305)
[2026-05-28T00:06:37] Filtering viral contigs with less than 5% coverage (remaining=2047305)
[2026-05-28T00:06:38] Estimating fragment length (mate gap mean=-88.7435, mate gap stddev=29.3603, read length mean=134.575)
[2026-05-28T00:06:39] Filtering read-through fragments with a distance <=10000bp (remaining=1899903)
[2026-05-28T00:06:39] Filtering inconsistently clipped mates (remaining=1868492)
[2026-05-28T00:06:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1823126)
[2026-05-28T00:06:41] Filtering fragments with small insert size (remaining=1822894)
[2026-05-28T00:06:42] Filtering alignments with long gaps (remaining=1822893)
[2026-05-28T00:06:43] Filtering fragments with both mates in the same gene (remaining=1822493)
[2026-05-28T00:06:43] Filtering fusions arising from hairpin structures (remaining=1713052)
[2026-05-28T00:06:44] Filtering reads with a mismatch p-value <=0.01 (remaining=762797)
[2026-05-28T00:06:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=338891)
[2026-05-28T00:06:53] Finding fusions and counting supporting reads (total=290296)
[2026-05-28T00:06:59] Merging adjacent fusion breakpoints (remaining=288505)
[2026-05-28T00:07:00] Filtering multi-mapping fusions by alignment score and read support (remaining=182331)
[2026-05-28T00:07:12] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:07:15] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=181084)
[2026-05-28T00:07:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=93079)
[2026-05-28T00:07:15] Filtering fusions with <2 supporting reads (remaining=10839)
[2026-05-28T00:07:16] Filtering fusions with an e-value >=0.3 (remaining=4244)
[2026-05-28T00:07:16] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4294)
[2026-05-28T00:07:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4254)
[2026-05-28T00:07:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4254)
[2026-05-28T00:07:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2605)
[2026-05-28T00:07:20] Searching for fusions with spliced split reads (remaining=2653)
[2026-05-28T00:07:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=1795)
[2026-05-28T00:07:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1767)
[2026-05-28T00:07:22] Searching for fusions with >=4 spliced events (remaining=1983)
[2026-05-28T00:07:23] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=746)
[2026-05-28T00:07:35] Filtering fusions with anchors <=23nt (remaining=603)
[2026-05-28T00:07:35] Filtering end-to-end fusions with low support (remaining=594)
[2026-05-28T00:07:35] Filtering fusions with no coverage around the breakpoints (remaining=568)
[2026-05-28T00:07:35] Indexing gene sequences 
[2026-05-28T00:07:39] Filtering genes with >=30% identity (remaining=197)
[2026-05-28T00:07:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=118)
[2026-05-28T00:07:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=114)
[2026-05-28T00:07:42] Searching for additional isoforms (remaining=134)
[2026-05-28T00:07:43] Assigning confidence scores to events 
[2026-05-28T00:07:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:07:44] Writing fusions to file 'tih_rna_sample_00096_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:07:45] Writing discarded fusions to file 'tih_rna_sample_00096_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:07:58] Freeing resources
[2026-05-28T00:08:05] Done (elapsed time=00:04:11, CPU time=00:04:10, peak memory=7.64gb)