[2026-06-08T08:49:53] Launching Arriba 2.4.0
[2026-06-08T08:49:53] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:50:03] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:50:08] Reading chimeric alignments from 'tih_rna_sample_00714_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=13100453)
[2026-06-08T08:57:50] Marking multi-mapping alignments (marked=8712812)
[2026-06-08T08:57:55] Detecting strandedness (reverse)
[2026-06-08T08:57:55] Assigning strands to alignments 
[2026-06-08T08:57:58] Annotating alignments 
[2026-06-08T08:58:55] Filtering duplicates (remaining=7351600)
[2026-06-08T08:59:05] 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=6867237)
[2026-06-08T08:59:08] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6867237)
[2026-06-08T08:59:11] Filtering viral contigs with expression lower than the top 5 (remaining=6867237)
[2026-06-08T08:59:17] Filtering viral contigs with less than 5% coverage (remaining=6867237)
[2026-06-08T08:59:20] Estimating fragment length (mate gap mean=-88.0931, mate gap stddev=29.4264, read length mean=132.891)
[2026-06-08T08:59:20] Filtering read-through fragments with a distance <=10000bp (remaining=6493541)
[2026-06-08T08:59:23] Filtering inconsistently clipped mates (remaining=6398771)
[2026-06-08T08:59:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6202810)
[2026-06-08T08:59:32] Filtering fragments with small insert size (remaining=6201999)
[2026-06-08T08:59:35] Filtering alignments with long gaps (remaining=6201999)
[2026-06-08T08:59:38] Filtering fragments with both mates in the same gene (remaining=6200922)
[2026-06-08T08:59:41] Filtering fusions arising from hairpin structures (remaining=5861653)
[2026-06-08T08:59:45] Filtering reads with a mismatch p-value <=0.01 (remaining=2699127)
[2026-06-08T09:00:02] Filtering reads with low entropy (k-mer content >=60%) (remaining=864516)
[2026-06-08T09:00:14] Finding fusions and counting supporting reads (total=674736)
[2026-06-08T09:00:35] Merging adjacent fusion breakpoints (remaining=667510)
[2026-06-08T09:00:37] Filtering multi-mapping fusions by alignment score and read support (remaining=413349)
[2026-06-08T09:01:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:01:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=410588)
[2026-06-08T09:01:29] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=232897)
[2026-06-08T09:01:30] Filtering fusions with <2 supporting reads (remaining=29624)
[2026-06-08T09:01:31] Filtering fusions with an e-value >=0.3 (remaining=9765)
[2026-06-08T09:01:32] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9815)
[2026-06-08T09:01:37] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9720)
[2026-06-08T09:01:37] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9720)
[2026-06-08T09:01:39] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6463)
[2026-06-08T09:01:46] Searching for fusions with spliced split reads (remaining=6483)
[2026-06-08T09:01:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=3903)
[2026-06-08T09:01:54] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3856)
[2026-06-08T09:01:55] Searching for fusions with >=4 spliced events (remaining=4670)
[2026-06-08T09:01:57] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2012)
[2026-06-08T09:02:10] Filtering fusions with anchors <=23nt (remaining=1594)
[2026-06-08T09:02:11] Filtering end-to-end fusions with low support (remaining=1505)
[2026-06-08T09:02:12] Filtering fusions with no coverage around the breakpoints (remaining=1452)
[2026-06-08T09:02:13] Indexing gene sequences 
[2026-06-08T09:02:19] Filtering genes with >=30% identity (remaining=434)
[2026-06-08T09:02:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=142)
[2026-06-08T09:02:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=130)
[2026-06-08T09:02:26] Searching for additional isoforms (remaining=175)
[2026-06-08T09:02:27] Assigning confidence scores to events 
[2026-06-08T09:02:31] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:02:31] Writing fusions to file 'tih_rna_sample_00714_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:02:33] Writing discarded fusions to file 'tih_rna_sample_00714_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:03:07] Freeing resources
[2026-06-08T09:03:29] Done (elapsed time=00:13:36, CPU time=00:13:34, peak memory=17.8gb)