[2026-06-08T08:35:36] Launching Arriba 2.4.0
[2026-06-08T08:35:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:49] Reading chimeric alignments from 'tih_rna_sample_00762_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10924581)
[2026-06-08T08:42:38] Marking multi-mapping alignments (marked=6949034)
[2026-06-08T08:42:43] Detecting strandedness (reverse)
[2026-06-08T08:42:43] Assigning strands to alignments 
[2026-06-08T08:42:45] Annotating alignments 
[2026-06-08T08:43:22] Filtering duplicates (remaining=7226060)
[2026-06-08T08:43:30] 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=6860319)
[2026-06-08T08:43:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6860319)
[2026-06-08T08:43:34] Filtering viral contigs with expression lower than the top 5 (remaining=6860319)
[2026-06-08T08:43:39] Filtering viral contigs with less than 5% coverage (remaining=6860319)
[2026-06-08T08:43:42] Estimating fragment length (mate gap mean=-87.0365, mate gap stddev=31.0266, read length mean=138)
[2026-06-08T08:43:42] Filtering read-through fragments with a distance <=10000bp (remaining=6523444)
[2026-06-08T08:43:45] Filtering inconsistently clipped mates (remaining=6425990)
[2026-06-08T08:43:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6283037)
[2026-06-08T08:43:52] Filtering fragments with small insert size (remaining=6282448)
[2026-06-08T08:43:54] Filtering alignments with long gaps (remaining=6282447)
[2026-06-08T08:43:56] Filtering fragments with both mates in the same gene (remaining=6281445)
[2026-06-08T08:43:59] Filtering fusions arising from hairpin structures (remaining=5883469)
[2026-06-08T08:44:01] Filtering reads with a mismatch p-value <=0.01 (remaining=3065109)
[2026-06-08T08:44:18] Filtering reads with low entropy (k-mer content >=60%) (remaining=983822)
[2026-06-08T08:44:30] Finding fusions and counting supporting reads (total=722028)
[2026-06-08T08:44:49] Merging adjacent fusion breakpoints (remaining=716709)
[2026-06-08T08:44:50] Filtering multi-mapping fusions by alignment score and read support (remaining=465223)
[2026-06-08T08:45:27] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:45:35] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=462301)
[2026-06-08T08:45:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=275819)
[2026-06-08T08:45:37] Filtering fusions with <2 supporting reads (remaining=39442)
[2026-06-08T08:45:38] Filtering fusions with an e-value >=0.3 (remaining=13723)
[2026-06-08T08:45:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13790)
[2026-06-08T08:45:43] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13719)
[2026-06-08T08:45:44] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13719)
[2026-06-08T08:45:46] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8422)
[2026-06-08T08:45:51] Searching for fusions with spliced split reads (remaining=8440)
[2026-06-08T08:45:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=4964)
[2026-06-08T08:45:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4920)
[2026-06-08T08:45:59] Searching for fusions with >=4 spliced events (remaining=5825)
[2026-06-08T08:46:00] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2042)
[2026-06-08T08:46:15] Filtering fusions with anchors <=23nt (remaining=1591)
[2026-06-08T08:46:16] Filtering end-to-end fusions with low support (remaining=1548)
[2026-06-08T08:46:17] Filtering fusions with no coverage around the breakpoints (remaining=1502)
[2026-06-08T08:46:18] Indexing gene sequences 
[2026-06-08T08:46:24] Filtering genes with >=30% identity (remaining=515)
[2026-06-08T08:46:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=272)
[2026-06-08T08:46:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=219)
[2026-06-08T08:46:31] Searching for additional isoforms (remaining=295)
[2026-06-08T08:46:33] Assigning confidence scores to events 
[2026-06-08T08:46:36] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:46:37] Writing fusions to file 'tih_rna_sample_00762_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:46:39] Writing discarded fusions to file 'tih_rna_sample_00762_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:12] Freeing resources
[2026-06-08T08:47:30] Done (elapsed time=00:11:54, CPU time=00:11:52, peak memory=15.5gb)