[2026-06-08T08:17:23] Launching Arriba 2.4.0
[2026-06-08T08:17:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:17:32] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:17:36] Reading chimeric alignments from 'tih_rna_sample_00464_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=7481839)
[2026-06-08T08:22:02] Marking multi-mapping alignments (marked=4760352)
[2026-06-08T08:22:05] Detecting strandedness (reverse)
[2026-06-08T08:22:05] Assigning strands to alignments 
[2026-06-08T08:22:07] Annotating alignments 
[2026-06-08T08:22:33] Filtering duplicates (remaining=3746506)
[2026-06-08T08:22:38] 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=3606581)
[2026-06-08T08:22:39] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3606581)
[2026-06-08T08:22:41] Filtering viral contigs with expression lower than the top 5 (remaining=3606581)
[2026-06-08T08:22:44] Filtering viral contigs with less than 5% coverage (remaining=3606581)
[2026-06-08T08:22:46] Estimating fragment length (mate gap mean=-85.1792, mate gap stddev=27.852, read length mean=126.707)
[2026-06-08T08:22:46] Filtering read-through fragments with a distance <=10000bp (remaining=3370306)
[2026-06-08T08:22:48] Filtering inconsistently clipped mates (remaining=3316378)
[2026-06-08T08:22:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3220063)
[2026-06-08T08:22:52] Filtering fragments with small insert size (remaining=3219489)
[2026-06-08T08:22:53] Filtering alignments with long gaps (remaining=3219489)
[2026-06-08T08:22:55] Filtering fragments with both mates in the same gene (remaining=3218823)
[2026-06-08T08:22:57] Filtering fusions arising from hairpin structures (remaining=3067709)
[2026-06-08T08:22:58] Filtering reads with a mismatch p-value <=0.01 (remaining=1312258)
[2026-06-08T08:23:07] Filtering reads with low entropy (k-mer content >=60%) (remaining=589519)
[2026-06-08T08:23:13] Finding fusions and counting supporting reads (total=495180)
[2026-06-08T08:23:27] Merging adjacent fusion breakpoints (remaining=491274)
[2026-06-08T08:23:28] Filtering multi-mapping fusions by alignment score and read support (remaining=294467)
[2026-06-08T08:23:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:23:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=293017)
[2026-06-08T08:23:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=156643)
[2026-06-08T08:24:00] Filtering fusions with <2 supporting reads (remaining=19426)
[2026-06-08T08:24:00] Filtering fusions with an e-value >=0.3 (remaining=5153)
[2026-06-08T08:24:01] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5186)
[2026-06-08T08:24:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5125)
[2026-06-08T08:24:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5125)
[2026-06-08T08:24:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4447)
[2026-06-08T08:24:08] Searching for fusions with spliced split reads (remaining=4520)
[2026-06-08T08:24:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=3129)
[2026-06-08T08:24:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3086)
[2026-06-08T08:24:13] Searching for fusions with >=4 spliced events (remaining=3537)
[2026-06-08T08:24:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1302)
[2026-06-08T08:24:26] Filtering fusions with anchors <=23nt (remaining=1124)
[2026-06-08T08:24:27] Filtering end-to-end fusions with low support (remaining=1090)
[2026-06-08T08:24:27] Filtering fusions with no coverage around the breakpoints (remaining=1059)
[2026-06-08T08:24:28] Indexing gene sequences 
[2026-06-08T08:24:32] Filtering genes with >=30% identity (remaining=371)
[2026-06-08T08:24:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=169)
[2026-06-08T08:24:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=131)
[2026-06-08T08:24:36] Searching for additional isoforms (remaining=157)
[2026-06-08T08:24:37] Assigning confidence scores to events 
[2026-06-08T08:24:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:24:39] Writing fusions to file 'tih_rna_sample_00464_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:24:40] Writing discarded fusions to file 'tih_rna_sample_00464_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:25:01] Freeing resources
[2026-06-08T08:25:14] Done (elapsed time=00:07:51, CPU time=00:07:49, peak memory=11.8gb)