[2026-06-08T07:28:58] Launching Arriba 2.4.0
[2026-06-08T07:28:58] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:29:11] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:29:16] Reading chimeric alignments from 'tih_rna_sample_00105_23H5VFLT4_s21.Aligned.sortedByCoord.out.bam' (total=4694652)
[2026-06-08T07:31:19] Marking multi-mapping alignments (marked=3693625)
[2026-06-08T07:31:22] Detecting strandedness (reverse)
[2026-06-08T07:31:22] Assigning strands to alignments 
[2026-06-08T07:31:23] Annotating alignments 
[2026-06-08T07:31:43] Filtering duplicates (remaining=2306730)
[2026-06-08T07:31:47] 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=2108150)
[2026-06-08T07:31:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2108150)
[2026-06-08T07:31:49] Filtering viral contigs with expression lower than the top 5 (remaining=2108150)
[2026-06-08T07:31:51] Filtering viral contigs with less than 5% coverage (remaining=2108150)
[2026-06-08T07:31:52] Estimating fragment length (mate gap mean=-68.5295, mate gap stddev=30.6326, read length mean=100.521)
[2026-06-08T07:31:52] Filtering read-through fragments with a distance <=10000bp (remaining=2038098)
[2026-06-08T07:31:53] Filtering inconsistently clipped mates (remaining=1976903)
[2026-06-08T07:31:54] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1643517)
[2026-06-08T07:31:57] Filtering fragments with small insert size (remaining=1641694)
[2026-06-08T07:31:58] Filtering alignments with long gaps (remaining=1641694)
[2026-06-08T07:31:59] Filtering fragments with both mates in the same gene (remaining=1640531)
[2026-06-08T07:32:00] Filtering fusions arising from hairpin structures (remaining=1522071)
[2026-06-08T07:32:01] Filtering reads with a mismatch p-value <=0.01 (remaining=332295)
[2026-06-08T07:32:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=231404)
[2026-06-08T07:32:08] Finding fusions and counting supporting reads (total=245749)
[2026-06-08T07:32:16] Merging adjacent fusion breakpoints (remaining=244901)
[2026-06-08T07:32:17] Filtering multi-mapping fusions by alignment score and read support (remaining=91503)
[2026-06-08T07:32:36] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:32:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=90677)
[2026-06-08T07:32:40] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=74526)
[2026-06-08T07:32:41] Filtering fusions with <2 supporting reads (remaining=1831)
[2026-06-08T07:32:41] Filtering fusions with an e-value >=0.3 (remaining=490)
[2026-06-08T07:32:41] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=501)
[2026-06-08T07:32:43] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=415)
[2026-06-08T07:32:44] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=415)
[2026-06-08T07:32:44] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=410)
[2026-06-08T07:32:47] Searching for fusions with spliced split reads (remaining=436)
[2026-06-08T07:32:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=340)
[2026-06-08T07:32:51] Filtering read-through fusions with breakpoints near the gene boundary (remaining=336)
[2026-06-08T07:32:51] Searching for fusions with >=4 spliced events (remaining=340)
[2026-06-08T07:32:52] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=101)
[2026-06-08T07:33:06] Filtering fusions with anchors <=23nt (remaining=81)
[2026-06-08T07:33:06] Filtering end-to-end fusions with low support (remaining=75)
[2026-06-08T07:33:07] Filtering fusions with no coverage around the breakpoints (remaining=72)
[2026-06-08T07:33:07] Indexing gene sequences 
[2026-06-08T07:33:08] Filtering genes with >=30% identity (remaining=31)
[2026-06-08T07:33:09] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=12)
[2026-06-08T07:33:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=12)
[2026-06-08T07:33:10] Searching for additional isoforms (remaining=14)
[2026-06-08T07:33:10] Assigning confidence scores to events 
[2026-06-08T07:33:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:33:12] Writing fusions to file 'tih_rna_sample_00105_23H5VFLT4_s21.arriba.fusions.tsv' 
[2026-06-08T07:33:13] Writing discarded fusions to file 'tih_rna_sample_00105_23H5VFLT4_s21.arriba.fusions.discarded.tsv'
[2026-06-08T07:33:29] Freeing resources
[2026-06-08T07:33:40] Done (elapsed time=00:04:42, CPU time=00:04:41, peak memory=9.23gb)