[2026-06-08T08:16:07] Launching Arriba 2.4.0
[2026-06-08T08:16:07] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:16:20] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:16:24] Reading chimeric alignments from 'tih_rna_sample_00461_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=7424939)
[2026-06-08T08:21:59] Marking multi-mapping alignments (marked=4890387)
[2026-06-08T08:22:02] Detecting strandedness (reverse)
[2026-06-08T08:22:02] Assigning strands to alignments 
[2026-06-08T08:22:03] Annotating alignments 
[2026-06-08T08:22:28] Filtering duplicates (remaining=4719561)
[2026-06-08T08:22:34] 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=4480137)
[2026-06-08T08:22:35] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4480137)
[2026-06-08T08:22:37] Filtering viral contigs with expression lower than the top 5 (remaining=4480137)
[2026-06-08T08:22:40] Filtering viral contigs with less than 5% coverage (remaining=4480137)
[2026-06-08T08:22:41] Estimating fragment length (mate gap mean=-85.7803, mate gap stddev=28.939, read length mean=131.256)
[2026-06-08T08:22:41] Filtering read-through fragments with a distance <=10000bp (remaining=4196277)
[2026-06-08T08:22:43] Filtering inconsistently clipped mates (remaining=4130565)
[2026-06-08T08:22:44] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4034820)
[2026-06-08T08:22:47] Filtering fragments with small insert size (remaining=4034143)
[2026-06-08T08:22:48] Filtering alignments with long gaps (remaining=4034143)
[2026-06-08T08:22:50] Filtering fragments with both mates in the same gene (remaining=4033265)
[2026-06-08T08:22:52] Filtering fusions arising from hairpin structures (remaining=3817250)
[2026-06-08T08:22:53] Filtering reads with a mismatch p-value <=0.01 (remaining=1748667)
[2026-06-08T08:23:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=761378)
[2026-06-08T08:23:10] Finding fusions and counting supporting reads (total=614419)
[2026-06-08T08:23:23] Merging adjacent fusion breakpoints (remaining=609919)
[2026-06-08T08:23:24] Filtering multi-mapping fusions by alignment score and read support (remaining=376519)
[2026-06-08T08:23:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:23:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=374473)
[2026-06-08T08:23:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=204654)
[2026-06-08T08:23:54] Filtering fusions with <2 supporting reads (remaining=26197)
[2026-06-08T08:23:55] Filtering fusions with an e-value >=0.3 (remaining=7721)
[2026-06-08T08:23:55] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7757)
[2026-06-08T08:23:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7682)
[2026-06-08T08:23:58] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7682)
[2026-06-08T08:23:59] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5629)
[2026-06-08T08:24:03] Searching for fusions with spliced split reads (remaining=5734)
[2026-06-08T08:24:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=3623)
[2026-06-08T08:24:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3590)
[2026-06-08T08:24:08] Searching for fusions with >=4 spliced events (remaining=4480)
[2026-06-08T08:24:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2014)
[2026-06-08T08:24:28] Filtering fusions with anchors <=23nt (remaining=1735)
[2026-06-08T08:24:29] Filtering end-to-end fusions with low support (remaining=1696)
[2026-06-08T08:24:29] Filtering fusions with no coverage around the breakpoints (remaining=1660)
[2026-06-08T08:24:30] Indexing gene sequences 
[2026-06-08T08:24:40] Filtering genes with >=30% identity (remaining=646)
[2026-06-08T08:24:46] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=397)
[2026-06-08T08:25:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=275)
[2026-06-08T08:25:04] Searching for additional isoforms (remaining=391)
[2026-06-08T08:25:05] Assigning confidence scores to events 
[2026-06-08T08:25:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:25:08] Writing fusions to file 'tih_rna_sample_00461_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:25:13] Writing discarded fusions to file 'tih_rna_sample_00461_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:25:41] Freeing resources
[2026-06-08T08:25:58] Done (elapsed time=00:09:51, CPU time=00:09:50, peak memory=12gb)