[2026-06-08T08:33:14] Launching Arriba 2.4.0
[2026-06-08T08:33:14] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:33:22] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:33:27] Reading chimeric alignments from 'tih_rna_sample_00136_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=8761983)
[2026-06-08T08:39:24] Marking multi-mapping alignments (marked=5586190)
[2026-06-08T08:39:28] Detecting strandedness (reverse)
[2026-06-08T08:39:28] Assigning strands to alignments 
[2026-06-08T08:39:30] Annotating alignments 
[2026-06-08T08:40:01] Filtering duplicates (remaining=3751808)
[2026-06-08T08:40:06] 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=3561621)
[2026-06-08T08:40:08] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3561621)
[2026-06-08T08:40:10] Filtering viral contigs with expression lower than the top 5 (remaining=3561621)
[2026-06-08T08:40:13] Filtering viral contigs with less than 5% coverage (remaining=3561621)
[2026-06-08T08:40:16] Estimating fragment length (mate gap mean=-88.391, mate gap stddev=28.8224, read length mean=134.167)
[2026-06-08T08:40:16] Filtering read-through fragments with a distance <=10000bp (remaining=3359343)
[2026-06-08T08:40:17] Filtering inconsistently clipped mates (remaining=3299054)
[2026-06-08T08:40:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3188436)
[2026-06-08T08:40:22] Filtering fragments with small insert size (remaining=3187958)
[2026-06-08T08:40:24] Filtering alignments with long gaps (remaining=3187958)
[2026-06-08T08:40:26] Filtering fragments with both mates in the same gene (remaining=3187228)
[2026-06-08T08:40:28] Filtering fusions arising from hairpin structures (remaining=3005621)
[2026-06-08T08:40:30] Filtering reads with a mismatch p-value <=0.01 (remaining=1324953)
[2026-06-08T08:40:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=579805)
[2026-06-08T08:40:46] Finding fusions and counting supporting reads (total=459884)
[2026-06-08T08:40:59] Merging adjacent fusion breakpoints (remaining=455887)
[2026-06-08T08:41:00] Filtering multi-mapping fusions by alignment score and read support (remaining=266410)
[2026-06-08T08:41:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:34] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=263191)
[2026-06-08T08:41:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=145902)
[2026-06-08T08:41:35] Filtering fusions with <2 supporting reads (remaining=20045)
[2026-06-08T08:41:35] Filtering fusions with an e-value >=0.3 (remaining=6425)
[2026-06-08T08:41:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6464)
[2026-06-08T08:41:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6365)
[2026-06-08T08:41:39] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6365)
[2026-06-08T08:41:40] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5194)
[2026-06-08T08:41:44] Searching for fusions with spliced split reads (remaining=5283)
[2026-06-08T08:41:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=3538)
[2026-06-08T08:41:49] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3491)
[2026-06-08T08:41:49] Searching for fusions with >=4 spliced events (remaining=4007)
[2026-06-08T08:41:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1227)
[2026-06-08T08:42:04] Filtering fusions with anchors <=23nt (remaining=1043)
[2026-06-08T08:42:04] Filtering end-to-end fusions with low support (remaining=1019)
[2026-06-08T08:42:05] Filtering fusions with no coverage around the breakpoints (remaining=994)
[2026-06-08T08:42:05] Indexing gene sequences 
[2026-06-08T08:42:10] Filtering genes with >=30% identity (remaining=365)
[2026-06-08T08:42:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=248)
[2026-06-08T08:42:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=221)
[2026-06-08T08:42:16] Searching for additional isoforms (remaining=260)
[2026-06-08T08:42:16] Assigning confidence scores to events 
[2026-06-08T08:42:19] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:42:19] Writing fusions to file 'tih_rna_sample_00136_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:42:20] Writing discarded fusions to file 'tih_rna_sample_00136_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:41] Freeing resources
[2026-06-08T08:42:55] Done (elapsed time=00:09:41, CPU time=00:09:39, peak memory=13.3gb)