[2026-06-08T08:49:21] Launching Arriba 2.4.0
[2026-06-08T08:49:21] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:34] Reading chimeric alignments from 'tih_rna_sample_00096_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9857695)
[2026-06-08T08:56:13] Marking multi-mapping alignments (marked=6305521)
[2026-06-08T08:56:17] Detecting strandedness (reverse)
[2026-06-08T08:56:17] Assigning strands to alignments 
[2026-06-08T08:56:19] Annotating alignments 
[2026-06-08T08:56:54] Filtering duplicates (remaining=4625607)
[2026-06-08T08:57:01] 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=4389901)
[2026-06-08T08:57:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4389901)
[2026-06-08T08:57:04] Filtering viral contigs with expression lower than the top 5 (remaining=4389901)
[2026-06-08T08:57:09] Filtering viral contigs with less than 5% coverage (remaining=4389901)
[2026-06-08T08:57:11] Estimating fragment length (mate gap mean=-88.3061, mate gap stddev=29.4692, read length mean=134.541)
[2026-06-08T08:57:11] Filtering read-through fragments with a distance <=10000bp (remaining=4117803)
[2026-06-08T08:57:13] Filtering inconsistently clipped mates (remaining=4055582)
[2026-06-08T08:57:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3935170)
[2026-06-08T08:57:19] Filtering fragments with small insert size (remaining=3934691)
[2026-06-08T08:57:21] Filtering alignments with long gaps (remaining=3934690)
[2026-06-08T08:57:23] Filtering fragments with both mates in the same gene (remaining=3933844)
[2026-06-08T08:57:25] Filtering fusions arising from hairpin structures (remaining=3735487)
[2026-06-08T08:57:28] Filtering reads with a mismatch p-value <=0.01 (remaining=1584773)
[2026-06-08T08:57:38] Filtering reads with low entropy (k-mer content >=60%) (remaining=647723)
[2026-06-08T08:57:46] Finding fusions and counting supporting reads (total=538290)
[2026-06-08T08:58:02] Merging adjacent fusion breakpoints (remaining=533976)
[2026-06-08T08:58:04] Filtering multi-mapping fusions by alignment score and read support (remaining=331825)
[2026-06-08T08:58:37] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:43] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=329570)
[2026-06-08T08:58:44] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=175420)
[2026-06-08T08:58:45] Filtering fusions with <2 supporting reads (remaining=20514)
[2026-06-08T08:58:45] Filtering fusions with an e-value >=0.3 (remaining=7392)
[2026-06-08T08:58:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7431)
[2026-06-08T08:58:49] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7350)
[2026-06-08T08:58:50] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7350)
[2026-06-08T08:58:51] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4359)
[2026-06-08T08:58:58] Searching for fusions with spliced split reads (remaining=4476)
[2026-06-08T08:59:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=2976)
[2026-06-08T08:59:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2935)
[2026-06-08T08:59:04] Searching for fusions with >=4 spliced events (remaining=3436)
[2026-06-08T08:59:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1436)
[2026-06-08T08:59:18] Filtering fusions with anchors <=23nt (remaining=1184)
[2026-06-08T08:59:18] Filtering end-to-end fusions with low support (remaining=1140)
[2026-06-08T08:59:19] Filtering fusions with no coverage around the breakpoints (remaining=1100)
[2026-06-08T08:59:20] Indexing gene sequences 
[2026-06-08T08:59:25] Filtering genes with >=30% identity (remaining=357)
[2026-06-08T08:59:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=178)
[2026-06-08T08:59:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=170)
[2026-06-08T08:59:31] Searching for additional isoforms (remaining=206)
[2026-06-08T08:59:33] Assigning confidence scores to events 
[2026-06-08T08:59:35] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:35] Writing fusions to file 'tih_rna_sample_00096_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:37] Writing discarded fusions to file 'tih_rna_sample_00096_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:02] Freeing resources
[2026-06-08T09:00:18] Done (elapsed time=00:10:57, CPU time=00:10:57, peak memory=14.4gb)