[2026-06-08T08:50:38] Launching Arriba 2.4.0
[2026-06-08T08:50:38] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:50:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:50:52] Reading chimeric alignments from 'tih_rna_sample_00730_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=12165645)
[2026-06-08T08:58:26] Marking multi-mapping alignments (marked=7751575)
[2026-06-08T08:58:32] Detecting strandedness (reverse)
[2026-06-08T08:58:32] Assigning strands to alignments 
[2026-06-08T08:58:34] Annotating alignments 
[2026-06-08T08:59:18] Filtering duplicates (remaining=7363102)
[2026-06-08T08:59:28] 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=6963742)
[2026-06-08T08:59:31] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6963742)
[2026-06-08T08:59:33] Filtering viral contigs with expression lower than the top 5 (remaining=6963742)
[2026-06-08T08:59:39] Filtering viral contigs with less than 5% coverage (remaining=6963742)
[2026-06-08T08:59:42] Estimating fragment length (mate gap mean=-87.5263, mate gap stddev=29.1053, read length mean=135.96)
[2026-06-08T08:59:43] Filtering read-through fragments with a distance <=10000bp (remaining=6521365)
[2026-06-08T08:59:45] Filtering inconsistently clipped mates (remaining=6420728)
[2026-06-08T08:59:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6291556)
[2026-06-08T08:59:54] Filtering fragments with small insert size (remaining=6290831)
[2026-06-08T08:59:57] Filtering alignments with long gaps (remaining=6290831)
[2026-06-08T09:00:00] Filtering fragments with both mates in the same gene (remaining=6289850)
[2026-06-08T09:00:03] Filtering fusions arising from hairpin structures (remaining=5910624)
[2026-06-08T09:00:07] Filtering reads with a mismatch p-value <=0.01 (remaining=2968998)
[2026-06-08T09:00:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=1019010)
[2026-06-08T09:00:37] Finding fusions and counting supporting reads (total=794212)
[2026-06-08T09:00:59] Merging adjacent fusion breakpoints (remaining=786775)
[2026-06-08T09:01:01] Filtering multi-mapping fusions by alignment score and read support (remaining=495864)
[2026-06-08T09:01:45] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:01:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=492044)
[2026-06-08T09:01:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=265507)
[2026-06-08T09:01:55] Filtering fusions with <2 supporting reads (remaining=41278)
[2026-06-08T09:01:56] Filtering fusions with an e-value >=0.3 (remaining=19313)
[2026-06-08T09:01:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=19373)
[2026-06-08T09:02:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=19293)
[2026-06-08T09:02:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=19293)
[2026-06-08T09:02:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6679)
[2026-06-08T09:02:13] Searching for fusions with spliced split reads (remaining=6801)
[2026-06-08T09:02:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=4115)
[2026-06-08T09:02:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4068)
[2026-06-08T09:02:23] Searching for fusions with >=4 spliced events (remaining=4837)
[2026-06-08T09:02:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1991)
[2026-06-08T09:02:41] Filtering fusions with anchors <=23nt (remaining=1601)
[2026-06-08T09:02:42] Filtering end-to-end fusions with low support (remaining=1546)
[2026-06-08T09:02:43] Filtering fusions with no coverage around the breakpoints (remaining=1511)
[2026-06-08T09:02:43] Indexing gene sequences 
[2026-06-08T09:02:50] Filtering genes with >=30% identity (remaining=516)
[2026-06-08T09:02:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=255)
[2026-06-08T09:02:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=200)
[2026-06-08T09:02:59] Searching for additional isoforms (remaining=275)
[2026-06-08T09:03:01] Assigning confidence scores to events 
[2026-06-08T09:03:05] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:03:05] Writing fusions to file 'tih_rna_sample_00730_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:03:07] Writing discarded fusions to file 'tih_rna_sample_00730_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:03:46] Freeing resources
[2026-06-08T09:04:08] Done (elapsed time=00:13:30, CPU time=00:13:28, peak memory=16.8gb)