[2026-06-08T08:30:40] Launching Arriba 2.4.0
[2026-06-08T08:30:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:52] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:30:55] Reading chimeric alignments from 'tih_rna_sample_00089_23H5VFLT4_s39.Aligned.sortedByCoord.out.bam' (total=9928878)
[2026-06-08T08:37:47] Marking multi-mapping alignments (marked=6419868)
[2026-06-08T08:37:52] Detecting strandedness (reverse)
[2026-06-08T08:37:52] Assigning strands to alignments 
[2026-06-08T08:37:53] Annotating alignments 
[2026-06-08T08:38:25] Filtering duplicates (remaining=6474308)
[2026-06-08T08:38:31] 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=6072135)
[2026-06-08T08:38:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6072135)
[2026-06-08T08:38:35] Filtering viral contigs with expression lower than the top 5 (remaining=6072135)
[2026-06-08T08:38:39] Filtering viral contigs with less than 5% coverage (remaining=6072135)
[2026-06-08T08:38:41] Estimating fragment length (mate gap mean=-87.6371, mate gap stddev=29.6304, read length mean=132.24)
[2026-06-08T08:38:41] Filtering read-through fragments with a distance <=10000bp (remaining=5618635)
[2026-06-08T08:38:43] Filtering inconsistently clipped mates (remaining=5494609)
[2026-06-08T08:38:44] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5135825)
[2026-06-08T08:38:49] Filtering fragments with small insert size (remaining=5134425)
[2026-06-08T08:38:51] Filtering alignments with long gaps (remaining=5134423)
[2026-06-08T08:38:53] Filtering fragments with both mates in the same gene (remaining=5133168)
[2026-06-08T08:38:55] Filtering fusions arising from hairpin structures (remaining=4691687)
[2026-06-08T08:38:57] Filtering reads with a mismatch p-value <=0.01 (remaining=2119617)
[2026-06-08T08:39:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=1326952)
[2026-06-08T08:39:22] Finding fusions and counting supporting reads (total=1092974)
[2026-06-08T08:39:38] Merging adjacent fusion breakpoints (remaining=1085241)
[2026-06-08T08:39:40] Filtering multi-mapping fusions by alignment score and read support (remaining=646902)
[2026-06-08T08:40:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:40:15] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=644220)
[2026-06-08T08:40:16] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=411633)
[2026-06-08T08:40:17] Filtering fusions with <2 supporting reads (remaining=34680)
[2026-06-08T08:40:18] Filtering fusions with an e-value >=0.3 (remaining=8291)
[2026-06-08T08:40:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8365)
[2026-06-08T08:40:22] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8178)
[2026-06-08T08:40:23] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8180)
[2026-06-08T08:40:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5850)
[2026-06-08T08:40:29] Searching for fusions with spliced split reads (remaining=5962)
[2026-06-08T08:40:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=3976)
[2026-06-08T08:40:35] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3945)
[2026-06-08T08:40:36] Searching for fusions with >=4 spliced events (remaining=4787)
[2026-06-08T08:40:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1973)
[2026-06-08T08:40:50] Filtering fusions with anchors <=23nt (remaining=1554)
[2026-06-08T08:40:51] Filtering end-to-end fusions with low support (remaining=1527)
[2026-06-08T08:40:52] Filtering fusions with no coverage around the breakpoints (remaining=1514)
[2026-06-08T08:40:52] Indexing gene sequences 
[2026-06-08T08:40:58] Filtering genes with >=30% identity (remaining=515)
[2026-06-08T08:41:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=255)
[2026-06-08T08:41:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=215)
[2026-06-08T08:41:07] Searching for additional isoforms (remaining=267)
[2026-06-08T08:41:08] Assigning confidence scores to events 
[2026-06-08T08:41:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:41:12] Writing fusions to file 'tih_rna_sample_00089_23H5VFLT4_s39.arriba.fusions.tsv' 
[2026-06-08T08:41:14] Writing discarded fusions to file 'tih_rna_sample_00089_23H5VFLT4_s39.arriba.fusions.discarded.tsv'
[2026-06-08T08:41:43] Freeing resources
[2026-06-08T08:42:00] Done (elapsed time=00:11:20, CPU time=00:11:20, peak memory=15.2gb)