[2026-06-08T08:02:19] Launching Arriba 2.4.0
[2026-06-08T08:02:19] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:02:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:02:46] Reading chimeric alignments from 'tih_rna_sample_00117_23H5VFLT4_s37.Aligned.sortedByCoord.out.bam' (total=7930388)
[2026-06-08T08:09:11] Marking multi-mapping alignments (marked=5527361)
[2026-06-08T08:09:15] Detecting strandedness (reverse)
[2026-06-08T08:09:15] Assigning strands to alignments 
[2026-06-08T08:09:16] Annotating alignments 
[2026-06-08T08:09:46] Filtering duplicates (remaining=2953569)
[2026-06-08T08:09:52] 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=2643324)
[2026-06-08T08:09:54] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2643324)
[2026-06-08T08:09:56] Filtering viral contigs with expression lower than the top 5 (remaining=2643324)
[2026-06-08T08:10:00] Filtering viral contigs with less than 5% coverage (remaining=2643324)
[2026-06-08T08:10:02] Estimating fragment length (mate gap mean=-84.4633, mate gap stddev=29.5135, read length mean=123.108)
[2026-06-08T08:10:02] Filtering read-through fragments with a distance <=10000bp (remaining=2525408)
[2026-06-08T08:10:03] Filtering inconsistently clipped mates (remaining=2467620)
[2026-06-08T08:10:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2172011)
[2026-06-08T08:10:08] Filtering fragments with small insert size (remaining=2171164)
[2026-06-08T08:10:10] Filtering alignments with long gaps (remaining=2171164)
[2026-06-08T08:10:11] Filtering fragments with both mates in the same gene (remaining=2170073)
[2026-06-08T08:10:13] Filtering fusions arising from hairpin structures (remaining=2036339)
[2026-06-08T08:10:15] Filtering reads with a mismatch p-value <=0.01 (remaining=709584)
[2026-06-08T08:10:21] Filtering reads with low entropy (k-mer content >=60%) (remaining=371215)
[2026-06-08T08:10:27] Finding fusions and counting supporting reads (total=351924)
[2026-06-08T08:10:38] Merging adjacent fusion breakpoints (remaining=350099)
[2026-06-08T08:10:39] Filtering multi-mapping fusions by alignment score and read support (remaining=164364)
[2026-06-08T08:11:04] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:11:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=162919)
[2026-06-08T08:11:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=116199)
[2026-06-08T08:11:09] Filtering fusions with <2 supporting reads (remaining=6433)
[2026-06-08T08:11:09] Filtering fusions with an e-value >=0.3 (remaining=1490)
[2026-06-08T08:11:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1516)
[2026-06-08T08:11:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1407)
[2026-06-08T08:11:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1407)
[2026-06-08T08:11:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1321)
[2026-06-08T08:11:16] Searching for fusions with spliced split reads (remaining=1422)
[2026-06-08T08:11:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=1107)
[2026-06-08T08:11:20] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1082)
[2026-06-08T08:11:21] Searching for fusions with >=4 spliced events (remaining=1144)
[2026-06-08T08:11:21] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=356)
[2026-06-08T08:11:35] Filtering fusions with anchors <=23nt (remaining=309)
[2026-06-08T08:11:36] Filtering end-to-end fusions with low support (remaining=304)
[2026-06-08T08:11:36] Filtering fusions with no coverage around the breakpoints (remaining=303)
[2026-06-08T08:11:36] Indexing gene sequences 
[2026-06-08T08:11:38] Filtering genes with >=30% identity (remaining=126)
[2026-06-08T08:11:39] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=86)
[2026-06-08T08:11:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=86)
[2026-06-08T08:11:41] Searching for additional isoforms (remaining=92)
[2026-06-08T08:11:42] Assigning confidence scores to events 
[2026-06-08T08:11:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:11:44] Writing fusions to file 'tih_rna_sample_00117_23H5VFLT4_s37.arriba.fusions.tsv' 
[2026-06-08T08:11:45] Writing discarded fusions to file 'tih_rna_sample_00117_23H5VFLT4_s37.arriba.fusions.discarded.tsv'
[2026-06-08T08:12:02] Freeing resources
[2026-06-08T08:12:16] Done (elapsed time=00:09:57, CPU time=00:09:56, peak memory=12.6gb)