[2026-05-28T00:02:50] Launching Arriba 2.4.0
[2026-05-28T00:02:50] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:03:03] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:03:08] Reading chimeric alignments from 'tih_rna_sample_00097_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=3785591)
[2026-05-28T00:06:20] Marking multi-mapping alignments (marked=2454978)
[2026-05-28T00:06:22] Detecting strandedness (no)
[2026-05-28T00:06:22] Annotating alignments 
[2026-05-28T00:06:43] Filtering duplicates (remaining=2462731)
[2026-05-28T00:06:47] 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=2366707)
[2026-05-28T00:06:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2366707)
[2026-05-28T00:06:48] Filtering viral contigs with expression lower than the top 5 (remaining=2366707)
[2026-05-28T00:06:50] Filtering viral contigs with less than 5% coverage (remaining=2366707)
[2026-05-28T00:06:51] Estimating fragment length (mate gap mean=-85.2628, mate gap stddev=27.0162, read length mean=124.625)
[2026-05-28T00:06:51] Filtering read-through fragments with a distance <=10000bp (remaining=2165300)
[2026-05-28T00:06:52] Filtering inconsistently clipped mates (remaining=2125125)
[2026-05-28T00:06:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2081356)
[2026-05-28T00:06:55] Filtering fragments with small insert size (remaining=2080961)
[2026-05-28T00:06:56] Filtering alignments with long gaps (remaining=2080961)
[2026-05-28T00:06:57] Filtering fragments with both mates in the same gene (remaining=2080511)
[2026-05-28T00:06:59] Filtering fusions arising from hairpin structures (remaining=1969253)
[2026-05-28T00:07:00] Filtering reads with a mismatch p-value <=0.01 (remaining=876372)
[2026-05-28T00:07:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=457871)
[2026-05-28T00:07:11] Finding fusions and counting supporting reads (total=382821)
[2026-05-28T00:07:20] Merging adjacent fusion breakpoints (remaining=377854)
[2026-05-28T00:07:21] Filtering multi-mapping fusions by alignment score and read support (remaining=219317)
[2026-05-28T00:07:38] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:07:42] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=218698)
[2026-05-28T00:07:43] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=114999)
[2026-05-28T00:07:43] Filtering fusions with <2 supporting reads (remaining=14448)
[2026-05-28T00:07:44] Filtering fusions with an e-value >=0.3 (remaining=3625)
[2026-05-28T00:07:44] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3671)
[2026-05-28T00:07:46] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3627)
[2026-05-28T00:07:46] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3627)
[2026-05-28T00:07:47] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3472)
[2026-05-28T00:07:49] Searching for fusions with spliced split reads (remaining=3493)
[2026-05-28T00:07:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=2409)
[2026-05-28T00:07:52] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2384)
[2026-05-28T00:07:53] Searching for fusions with >=4 spliced events (remaining=2686)
[2026-05-28T00:07:54] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1132)
[2026-05-28T00:08:15] Filtering fusions with anchors <=23nt (remaining=976)
[2026-05-28T00:08:15] Filtering end-to-end fusions with low support (remaining=950)
[2026-05-28T00:08:16] Filtering fusions with no coverage around the breakpoints (remaining=928)
[2026-05-28T00:08:16] Indexing gene sequences 
[2026-05-28T00:08:21] Filtering genes with >=30% identity (remaining=327)
[2026-05-28T00:08:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=129)
[2026-05-28T00:08:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=126)
[2026-05-28T00:08:24] Searching for additional isoforms (remaining=153)
[2026-05-28T00:08:25] Assigning confidence scores to events 
[2026-05-28T00:08:27] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:08:27] Writing fusions to file 'tih_rna_sample_00097_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-05-28T00:08:29] Writing discarded fusions to file 'tih_rna_sample_00097_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T00:08:48] Freeing resources
[2026-05-28T00:08:56] Done (elapsed time=00:06:06, CPU time=00:06:05, peak memory=8.11gb)