[2026-06-08T08:56:35] Launching Arriba 2.4.0
[2026-06-08T08:56:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:56:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:56:51] Reading chimeric alignments from 'tih_rna_sample_00686_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11649782)
[2026-06-08T09:04:08] Marking multi-mapping alignments (marked=7314966)
[2026-06-08T09:04:13] Detecting strandedness (reverse)
[2026-06-08T09:04:13] Assigning strands to alignments 
[2026-06-08T09:04:15] Annotating alignments 
[2026-06-08T09:04:49] Filtering duplicates (remaining=8013792)
[2026-06-08T09:04:57] 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=7673430)
[2026-06-08T09:04:59] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7673430)
[2026-06-08T09:05:01] Filtering viral contigs with expression lower than the top 5 (remaining=7673430)
[2026-06-08T09:05:06] Filtering viral contigs with less than 5% coverage (remaining=7673430)
[2026-06-08T09:05:09] Estimating fragment length (mate gap mean=-84.226, mate gap stddev=32.0882, read length mean=138.723)
[2026-06-08T09:05:09] Filtering read-through fragments with a distance <=10000bp (remaining=7289409)
[2026-06-08T09:05:11] Filtering inconsistently clipped mates (remaining=7200657)
[2026-06-08T09:05:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7038695)
[2026-06-08T09:05:18] Filtering fragments with small insert size (remaining=7037879)
[2026-06-08T09:05:21] Filtering alignments with long gaps (remaining=7037879)
[2026-06-08T09:05:23] Filtering fragments with both mates in the same gene (remaining=7036699)
[2026-06-08T09:05:25] Filtering fusions arising from hairpin structures (remaining=6666350)
[2026-06-08T09:05:28] Filtering reads with a mismatch p-value <=0.01 (remaining=3378375)
[2026-06-08T09:05:45] Filtering reads with low entropy (k-mer content >=60%) (remaining=1115567)
[2026-06-08T09:05:58] Finding fusions and counting supporting reads (total=840276)
[2026-06-08T09:06:17] Merging adjacent fusion breakpoints (remaining=831808)
[2026-06-08T09:06:18] Filtering multi-mapping fusions by alignment score and read support (remaining=558349)
[2026-06-08T09:06:51] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:06:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=555378)
[2026-06-08T09:07:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=310853)
[2026-06-08T09:07:02] Filtering fusions with <2 supporting reads (remaining=44582)
[2026-06-08T09:07:03] Filtering fusions with an e-value >=0.3 (remaining=17767)
[2026-06-08T09:07:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=17829)
[2026-06-08T09:07:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=17748)
[2026-06-08T09:07:09] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=17749)
[2026-06-08T09:07:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9145)
[2026-06-08T09:07:17] Searching for fusions with spliced split reads (remaining=9165)
[2026-06-08T09:07:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=4462)
[2026-06-08T09:07:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4409)
[2026-06-08T09:07:25] Searching for fusions with >=4 spliced events (remaining=5436)
[2026-06-08T09:07:27] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2013)
[2026-06-08T09:07:43] Filtering fusions with anchors <=23nt (remaining=1576)
[2026-06-08T09:07:44] Filtering end-to-end fusions with low support (remaining=1526)
[2026-06-08T09:07:45] Filtering fusions with no coverage around the breakpoints (remaining=1491)
[2026-06-08T09:07:45] Indexing gene sequences 
[2026-06-08T09:07:50] Filtering genes with >=30% identity (remaining=415)
[2026-06-08T09:07:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=182)
[2026-06-08T09:07:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=174)
[2026-06-08T09:07:58] Searching for additional isoforms (remaining=222)
[2026-06-08T09:08:00] Assigning confidence scores to events 
[2026-06-08T09:08:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:08:04] Writing fusions to file 'tih_rna_sample_00686_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:08:06] Writing discarded fusions to file 'tih_rna_sample_00686_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:08:40] Freeing resources
[2026-06-08T09:09:00] Done (elapsed time=00:12:25, CPU time=00:12:24, peak memory=16.3gb)