[2026-06-08T08:38:19] Launching Arriba 2.4.0
[2026-06-08T08:38:19] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:38:28] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:38:32] Reading chimeric alignments from 'tih_rna_sample_00121_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10167792)
[2026-06-08T08:45:10] Marking multi-mapping alignments (marked=6459166)
[2026-06-08T08:45:14] Detecting strandedness (reverse)
[2026-06-08T08:45:14] Assigning strands to alignments 
[2026-06-08T08:45:16] Annotating alignments 
[2026-06-08T08:45:52] Filtering duplicates (remaining=4167922)
[2026-06-08T08:45:58] 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=3941699)
[2026-06-08T08:46:00] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3941699)
[2026-06-08T08:46:03] Filtering viral contigs with expression lower than the top 5 (remaining=3941699)
[2026-06-08T08:46:07] Filtering viral contigs with less than 5% coverage (remaining=3941699)
[2026-06-08T08:46:10] Estimating fragment length (mate gap mean=-87.2492, mate gap stddev=29.2017, read length mean=131.578)
[2026-06-08T08:46:10] Filtering read-through fragments with a distance <=10000bp (remaining=3703356)
[2026-06-08T08:46:12] Filtering inconsistently clipped mates (remaining=3639015)
[2026-06-08T08:46:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3516592)
[2026-06-08T08:46:18] Filtering fragments with small insert size (remaining=3516000)
[2026-06-08T08:46:20] Filtering alignments with long gaps (remaining=3516000)
[2026-06-08T08:46:22] Filtering fragments with both mates in the same gene (remaining=3515243)
[2026-06-08T08:46:24] Filtering fusions arising from hairpin structures (remaining=3330519)
[2026-06-08T08:46:27] Filtering reads with a mismatch p-value <=0.01 (remaining=1390709)
[2026-06-08T08:46:37] Filtering reads with low entropy (k-mer content >=60%) (remaining=595749)
[2026-06-08T08:46:45] Finding fusions and counting supporting reads (total=480548)
[2026-06-08T08:47:01] Merging adjacent fusion breakpoints (remaining=476741)
[2026-06-08T08:47:02] Filtering multi-mapping fusions by alignment score and read support (remaining=297898)
[2026-06-08T08:47:36] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:47:41] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=295899)
[2026-06-08T08:47:42] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=159878)
[2026-06-08T08:47:43] Filtering fusions with <2 supporting reads (remaining=22393)
[2026-06-08T08:47:43] Filtering fusions with an e-value >=0.3 (remaining=7168)
[2026-06-08T08:47:44] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7219)
[2026-06-08T08:47:47] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7135)
[2026-06-08T08:47:47] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7135)
[2026-06-08T08:47:49] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4883)
[2026-06-08T08:47:53] Searching for fusions with spliced split reads (remaining=4960)
[2026-06-08T08:47:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=3347)
[2026-06-08T08:47:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3303)
[2026-06-08T08:47:58] Searching for fusions with >=4 spliced events (remaining=3761)
[2026-06-08T08:48:00] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1171)
[2026-06-08T08:48:12] Filtering fusions with anchors <=23nt (remaining=978)
[2026-06-08T08:48:13] Filtering end-to-end fusions with low support (remaining=951)
[2026-06-08T08:48:13] Filtering fusions with no coverage around the breakpoints (remaining=931)
[2026-06-08T08:48:14] Indexing gene sequences 
[2026-06-08T08:48:18] Filtering genes with >=30% identity (remaining=330)
[2026-06-08T08:48:21] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=192)
[2026-06-08T08:48:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=178)
[2026-06-08T08:48:24] Searching for additional isoforms (remaining=216)
[2026-06-08T08:48:25] Assigning confidence scores to events 
[2026-06-08T08:48:27] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:48:27] Writing fusions to file 'tih_rna_sample_00121_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:48:29] Writing discarded fusions to file 'tih_rna_sample_00121_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:48:51] Freeing resources
[2026-06-08T08:49:08] Done (elapsed time=00:10:49, CPU time=00:10:47, peak memory=14.7gb)