[2026-06-08T08:49:19] Launching Arriba 2.4.0
[2026-06-08T08:49:19] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:34] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:38] Reading chimeric alignments from 'tih_rna_sample_00462_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9236003)
[2026-06-08T08:57:50] Marking multi-mapping alignments (marked=5613803)
[2026-06-08T08:57:54] Detecting strandedness (reverse)
[2026-06-08T08:57:54] Assigning strands to alignments 
[2026-06-08T08:57:56] Annotating alignments 
[2026-06-08T08:58:30] Filtering duplicates (remaining=4466184)
[2026-06-08T08:58:35] 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=4283419)
[2026-06-08T08:58:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4283419)
[2026-06-08T08:58:39] Filtering viral contigs with expression lower than the top 5 (remaining=4283419)
[2026-06-08T08:58:44] Filtering viral contigs with less than 5% coverage (remaining=4283419)
[2026-06-08T08:58:46] Estimating fragment length (mate gap mean=-87.2828, mate gap stddev=28.9941, read length mean=134.644)
[2026-06-08T08:58:46] Filtering read-through fragments with a distance <=10000bp (remaining=4003486)
[2026-06-08T08:58:48] Filtering inconsistently clipped mates (remaining=3946817)
[2026-06-08T08:58:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3843397)
[2026-06-08T08:58:54] Filtering fragments with small insert size (remaining=3842829)
[2026-06-08T08:58:56] Filtering alignments with long gaps (remaining=3842828)
[2026-06-08T08:58:58] Filtering fragments with both mates in the same gene (remaining=3842094)
[2026-06-08T08:59:00] Filtering fusions arising from hairpin structures (remaining=3653717)
[2026-06-08T08:59:02] Filtering reads with a mismatch p-value <=0.01 (remaining=1575233)
[2026-06-08T08:59:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=655926)
[2026-06-08T08:59:21] Finding fusions and counting supporting reads (total=532316)
[2026-06-08T08:59:37] Merging adjacent fusion breakpoints (remaining=527553)
[2026-06-08T08:59:38] Filtering multi-mapping fusions by alignment score and read support (remaining=356099)
[2026-06-08T09:00:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=354365)
[2026-06-08T09:00:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=177697)
[2026-06-08T09:00:16] Filtering fusions with <2 supporting reads (remaining=25632)
[2026-06-08T09:00:16] Filtering fusions with an e-value >=0.3 (remaining=7976)
[2026-06-08T09:00:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8011)
[2026-06-08T09:00:20] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7935)
[2026-06-08T09:00:21] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7935)
[2026-06-08T09:00:22] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5495)
[2026-06-08T09:00:26] Searching for fusions with spliced split reads (remaining=5585)
[2026-06-08T09:00:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=3725)
[2026-06-08T09:00:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3663)
[2026-06-08T09:00:31] Searching for fusions with >=4 spliced events (remaining=4256)
[2026-06-08T09:00:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1496)
[2026-06-08T09:00:51] Filtering fusions with anchors <=23nt (remaining=1117)
[2026-06-08T09:00:52] Filtering end-to-end fusions with low support (remaining=1086)
[2026-06-08T09:00:52] Filtering fusions with no coverage around the breakpoints (remaining=1062)
[2026-06-08T09:00:53] Indexing gene sequences 
[2026-06-08T09:00:58] Filtering genes with >=30% identity (remaining=331)
[2026-06-08T09:01:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=160)
[2026-06-08T09:01:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=146)
[2026-06-08T09:01:05] Searching for additional isoforms (remaining=181)
[2026-06-08T09:01:06] Assigning confidence scores to events 
[2026-06-08T09:01:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:09] Writing fusions to file 'tih_rna_sample_00462_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:01:10] Writing discarded fusions to file 'tih_rna_sample_00462_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:36] Freeing resources
[2026-06-08T09:01:52] Done (elapsed time=00:12:33, CPU time=00:12:32, peak memory=13.7gb)