[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_00434_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=9853032)
[2026-06-08T08:56:07] Marking multi-mapping alignments (marked=6083831)
[2026-06-08T08:56:11] Detecting strandedness (reverse)
[2026-06-08T08:56:11] Assigning strands to alignments 
[2026-06-08T08:56:13] Annotating alignments 
[2026-06-08T08:56:45] Filtering duplicates (remaining=4819657)
[2026-06-08T08:56:50] 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=4622067)
[2026-06-08T08:56:52] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4622067)
[2026-06-08T08:56:54] Filtering viral contigs with expression lower than the top 5 (remaining=4622067)
[2026-06-08T08:56:58] Filtering viral contigs with less than 5% coverage (remaining=4622067)
[2026-06-08T08:57:00] Estimating fragment length (mate gap mean=-87.3469, mate gap stddev=27.9657, read length mean=131.647)
[2026-06-08T08:57:00] Filtering read-through fragments with a distance <=10000bp (remaining=4275445)
[2026-06-08T08:57:02] Filtering inconsistently clipped mates (remaining=4205820)
[2026-06-08T08:57:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4103034)
[2026-06-08T08:57:07] Filtering fragments with small insert size (remaining=4102356)
[2026-06-08T08:57:09] Filtering alignments with long gaps (remaining=4102354)
[2026-06-08T08:57:11] Filtering fragments with both mates in the same gene (remaining=4101536)
[2026-06-08T08:57:13] Filtering fusions arising from hairpin structures (remaining=3884339)
[2026-06-08T08:57:16] Filtering reads with a mismatch p-value <=0.01 (remaining=1789028)
[2026-06-08T08:57:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=870808)
[2026-06-08T08:57:35] Finding fusions and counting supporting reads (total=675919)
[2026-06-08T08:57:50] Merging adjacent fusion breakpoints (remaining=669663)
[2026-06-08T08:57:51] Filtering multi-mapping fusions by alignment score and read support (remaining=431773)
[2026-06-08T08:58:23] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=429903)
[2026-06-08T08:58:29] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=213465)
[2026-06-08T08:58:30] Filtering fusions with <2 supporting reads (remaining=31563)
[2026-06-08T08:58:31] Filtering fusions with an e-value >=0.3 (remaining=9286)
[2026-06-08T08:58:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9333)
[2026-06-08T08:58:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9259)
[2026-06-08T08:58:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9259)
[2026-06-08T08:58:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7140)
[2026-06-08T08:58:41] Searching for fusions with spliced split reads (remaining=7243)
[2026-06-08T08:58:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=4557)
[2026-06-08T08:58:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4503)
[2026-06-08T08:58:47] Searching for fusions with >=4 spliced events (remaining=5265)
[2026-06-08T08:58:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1787)
[2026-06-08T08:59:01] Filtering fusions with anchors <=23nt (remaining=1466)
[2026-06-08T08:59:01] Filtering end-to-end fusions with low support (remaining=1427)
[2026-06-08T08:59:02] Filtering fusions with no coverage around the breakpoints (remaining=1404)
[2026-06-08T08:59:02] Indexing gene sequences 
[2026-06-08T08:59:08] Filtering genes with >=30% identity (remaining=441)
[2026-06-08T08:59:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=186)
[2026-06-08T08:59:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=180)
[2026-06-08T08:59:15] Searching for additional isoforms (remaining=210)
[2026-06-08T08:59:16] Assigning confidence scores to events 
[2026-06-08T08:59:19] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:19] Writing fusions to file 'tih_rna_sample_00434_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:59:21] Writing discarded fusions to file 'tih_rna_sample_00434_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:45] Freeing resources
[2026-06-08T09:00:01] Done (elapsed time=00:10:40, CPU time=00:10:39, peak memory=14.5gb)