[2026-06-08T08:42:39] Launching Arriba 2.4.0
[2026-06-08T08:42:39] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:42:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:42:52] Reading chimeric alignments from 'tih_rna_sample_00699_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10323731)
[2026-06-08T08:49:32] Marking multi-mapping alignments (marked=6338244)
[2026-06-08T08:49:36] Detecting strandedness (reverse)
[2026-06-08T08:49:36] Assigning strands to alignments 
[2026-06-08T08:49:38] Annotating alignments 
[2026-06-08T08:50:10] Filtering duplicates (remaining=7283951)
[2026-06-08T08:50:17] 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=6978144)
[2026-06-08T08:50:19] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6978144)
[2026-06-08T08:50:21] Filtering viral contigs with expression lower than the top 5 (remaining=6978144)
[2026-06-08T08:50:25] Filtering viral contigs with less than 5% coverage (remaining=6978144)
[2026-06-08T08:50:27] Estimating fragment length (mate gap mean=-85.9497, mate gap stddev=31.3641, read length mean=137.433)
[2026-06-08T08:50:28] Filtering read-through fragments with a distance <=10000bp (remaining=6555125)
[2026-06-08T08:50:30] Filtering inconsistently clipped mates (remaining=6459072)
[2026-06-08T08:50:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6304787)
[2026-06-08T08:50:36] Filtering fragments with small insert size (remaining=6304180)
[2026-06-08T08:50:37] Filtering alignments with long gaps (remaining=6304176)
[2026-06-08T08:50:39] Filtering fragments with both mates in the same gene (remaining=6302996)
[2026-06-08T08:50:42] Filtering fusions arising from hairpin structures (remaining=5942385)
[2026-06-08T08:50:44] Filtering reads with a mismatch p-value <=0.01 (remaining=3098394)
[2026-06-08T08:51:00] Filtering reads with low entropy (k-mer content >=60%) (remaining=1096312)
[2026-06-08T08:51:11] Finding fusions and counting supporting reads (total=813084)
[2026-06-08T08:51:29] Merging adjacent fusion breakpoints (remaining=805979)
[2026-06-08T08:51:30] Filtering multi-mapping fusions by alignment score and read support (remaining=533132)
[2026-06-08T08:52:04] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:52:12] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=530477)
[2026-06-08T08:52:13] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=288395)
[2026-06-08T08:52:14] Filtering fusions with <2 supporting reads (remaining=40962)
[2026-06-08T08:52:15] Filtering fusions with an e-value >=0.3 (remaining=15458)
[2026-06-08T08:52:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=15517)
[2026-06-08T08:52:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=15421)
[2026-06-08T08:52:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=15422)
[2026-06-08T08:52:22] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9647)
[2026-06-08T08:52:26] Searching for fusions with spliced split reads (remaining=9681)
[2026-06-08T08:52:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=4797)
[2026-06-08T08:52:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4738)
[2026-06-08T08:52:33] Searching for fusions with >=4 spliced events (remaining=5962)
[2026-06-08T08:52:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2637)
[2026-06-08T08:52:49] Filtering fusions with anchors <=23nt (remaining=2175)
[2026-06-08T08:52:50] Filtering end-to-end fusions with low support (remaining=2124)
[2026-06-08T08:52:50] Filtering fusions with no coverage around the breakpoints (remaining=2054)
[2026-06-08T08:52:51] Indexing gene sequences 
[2026-06-08T08:52:58] Filtering genes with >=30% identity (remaining=735)
[2026-06-08T08:53:03] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=419)
[2026-06-08T08:53:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=291)
[2026-06-08T08:53:09] Searching for additional isoforms (remaining=418)
[2026-06-08T08:53:11] Assigning confidence scores to events 
[2026-06-08T08:53:14] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:53:14] Writing fusions to file 'tih_rna_sample_00699_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:53:18] Writing discarded fusions to file 'tih_rna_sample_00699_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:53:47] Freeing resources
[2026-06-08T08:54:04] Done (elapsed time=00:11:25, CPU time=00:11:24, peak memory=14.9gb)