[2026-06-08T08:24:27] Launching Arriba 2.4.0
[2026-06-08T08:24:27] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:24:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:24:40] Reading chimeric alignments from 'tih_rna_sample_00691_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=9837904)
[2026-06-08T08:30:32] Marking multi-mapping alignments (marked=6336018)
[2026-06-08T08:30:36] Detecting strandedness (reverse)
[2026-06-08T08:30:36] Assigning strands to alignments 
[2026-06-08T08:30:39] Annotating alignments 
[2026-06-08T08:31:15] Filtering duplicates (remaining=6436718)
[2026-06-08T08:31:24] 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=6080120)
[2026-06-08T08:31:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6080120)
[2026-06-08T08:31:28] Filtering viral contigs with expression lower than the top 5 (remaining=6080120)
[2026-06-08T08:31:33] Filtering viral contigs with less than 5% coverage (remaining=6080120)
[2026-06-08T08:31:36] Estimating fragment length (mate gap mean=-86.575, mate gap stddev=28.7069, read length mean=130.835)
[2026-06-08T08:31:36] Filtering read-through fragments with a distance <=10000bp (remaining=5733537)
[2026-06-08T08:31:39] Filtering inconsistently clipped mates (remaining=5636294)
[2026-06-08T08:31:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5532184)
[2026-06-08T08:31:46] Filtering fragments with small insert size (remaining=5531411)
[2026-06-08T08:31:48] Filtering alignments with long gaps (remaining=5531411)
[2026-06-08T08:31:50] Filtering fragments with both mates in the same gene (remaining=5530540)
[2026-06-08T08:31:53] Filtering fusions arising from hairpin structures (remaining=5195243)
[2026-06-08T08:31:55] Filtering reads with a mismatch p-value <=0.01 (remaining=2580949)
[2026-06-08T08:32:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=957113)
[2026-06-08T08:32:20] Finding fusions and counting supporting reads (total=684003)
[2026-06-08T08:32:38] Merging adjacent fusion breakpoints (remaining=675277)
[2026-06-08T08:32:40] Filtering multi-mapping fusions by alignment score and read support (remaining=421069)
[2026-06-08T08:33:15] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:33:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=419055)
[2026-06-08T08:33:23] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=231147)
[2026-06-08T08:33:25] Filtering fusions with <2 supporting reads (remaining=33360)
[2026-06-08T08:33:25] Filtering fusions with an e-value >=0.3 (remaining=8974)
[2026-06-08T08:33:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9028)
[2026-06-08T08:33:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8940)
[2026-06-08T08:33:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8940)
[2026-06-08T08:33:32] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8414)
[2026-06-08T08:33:38] Searching for fusions with spliced split reads (remaining=8509)
[2026-06-08T08:33:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=4927)
[2026-06-08T08:33:44] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4874)
[2026-06-08T08:33:45] Searching for fusions with >=4 spliced events (remaining=5814)
[2026-06-08T08:33:47] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2174)
[2026-06-08T08:34:03] Filtering fusions with anchors <=23nt (remaining=1737)
[2026-06-08T08:34:04] Filtering end-to-end fusions with low support (remaining=1673)
[2026-06-08T08:34:05] Filtering fusions with no coverage around the breakpoints (remaining=1638)
[2026-06-08T08:34:05] Indexing gene sequences 
[2026-06-08T08:34:11] Filtering genes with >=30% identity (remaining=467)
[2026-06-08T08:34:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=182)
[2026-06-08T08:34:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=172)
[2026-06-08T08:34:20] Searching for additional isoforms (remaining=202)
[2026-06-08T08:34:21] Assigning confidence scores to events 
[2026-06-08T08:34:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:34:25] Writing fusions to file 'tih_rna_sample_00691_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:34:27] Writing discarded fusions to file 'tih_rna_sample_00691_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:35:02] Freeing resources
[2026-06-08T08:35:20] Done (elapsed time=00:10:53, CPU time=00:10:51, peak memory=14.4gb)