[2026-06-08T08:40:17] Launching Arriba 2.4.0
[2026-06-08T08:40:17] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:40:25] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:30] Reading chimeric alignments from 'tih_rna_sample_00116_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=12197080)
[2026-06-08T08:47:00] Marking multi-mapping alignments (marked=7800226)
[2026-06-08T08:47:05] Detecting strandedness (reverse)
[2026-06-08T08:47:05] Assigning strands to alignments 
[2026-06-08T08:47:07] Annotating alignments 
[2026-06-08T08:47:49] Filtering duplicates (remaining=3648194)
[2026-06-08T08:47:55] 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=3376911)
[2026-06-08T08:47:58] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3376911)
[2026-06-08T08:48:00] Filtering viral contigs with expression lower than the top 5 (remaining=3376911)
[2026-06-08T08:48:05] Filtering viral contigs with less than 5% coverage (remaining=3376911)
[2026-06-08T08:48:08] Estimating fragment length (mate gap mean=-87.6091, mate gap stddev=26.9571, read length mean=124.647)
[2026-06-08T08:48:08] Filtering read-through fragments with a distance <=10000bp (remaining=3161039)
[2026-06-08T08:48:11] Filtering inconsistently clipped mates (remaining=3105806)
[2026-06-08T08:48:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2989045)
[2026-06-08T08:48:17] Filtering fragments with small insert size (remaining=2988155)
[2026-06-08T08:48:20] Filtering alignments with long gaps (remaining=2988155)
[2026-06-08T08:48:22] Filtering fragments with both mates in the same gene (remaining=2987465)
[2026-06-08T08:48:24] Filtering fusions arising from hairpin structures (remaining=2869063)
[2026-06-08T08:48:27] Filtering reads with a mismatch p-value <=0.01 (remaining=1040801)
[2026-06-08T08:48:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=473829)
[2026-06-08T08:48:43] Finding fusions and counting supporting reads (total=424272)
[2026-06-08T08:49:00] Merging adjacent fusion breakpoints (remaining=418181)
[2026-06-08T08:49:01] Filtering multi-mapping fusions by alignment score and read support (remaining=239203)
[2026-06-08T08:49:40] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:45] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=238159)
[2026-06-08T08:49:45] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=127627)
[2026-06-08T08:49:46] Filtering fusions with <2 supporting reads (remaining=13274)
[2026-06-08T08:49:46] Filtering fusions with an e-value >=0.3 (remaining=3187)
[2026-06-08T08:49:47] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3214)
[2026-06-08T08:49:50] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3140)
[2026-06-08T08:49:51] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3140)
[2026-06-08T08:49:52] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3077)
[2026-06-08T08:49:57] Searching for fusions with spliced split reads (remaining=3210)
[2026-06-08T08:50:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=2387)
[2026-06-08T08:50:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2361)
[2026-06-08T08:50:03] Searching for fusions with >=4 spliced events (remaining=2623)
[2026-06-08T08:50:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1024)
[2026-06-08T08:50:19] Filtering fusions with anchors <=23nt (remaining=714)
[2026-06-08T08:50:20] Filtering end-to-end fusions with low support (remaining=680)
[2026-06-08T08:50:20] Filtering fusions with no coverage around the breakpoints (remaining=662)
[2026-06-08T08:50:21] Indexing gene sequences 
[2026-06-08T08:50:24] Filtering genes with >=30% identity (remaining=241)
[2026-06-08T08:50:26] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=73)
[2026-06-08T08:50:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=73)
[2026-06-08T08:50:28] Searching for additional isoforms (remaining=82)
[2026-06-08T08:50:29] Assigning confidence scores to events 
[2026-06-08T08:50:31] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:50:31] Writing fusions to file 'tih_rna_sample_00116_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:50:32] Writing discarded fusions to file 'tih_rna_sample_00116_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:52] Freeing resources
[2026-06-08T08:51:10] Done (elapsed time=00:10:53, CPU time=00:10:53, peak memory=16.8gb)