[2026-06-08T08:39:27] Launching Arriba 2.4.0
[2026-06-08T08:39:27] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:48] Reading chimeric alignments from 'tih_rna_sample_00592_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=9996378)
[2026-06-08T08:48:12] Marking multi-mapping alignments (marked=6215579)
[2026-06-08T08:48:17] Detecting strandedness (reverse)
[2026-06-08T08:48:17] Assigning strands to alignments 
[2026-06-08T08:48:20] Annotating alignments 
[2026-06-08T08:49:06] Filtering duplicates (remaining=5623607)
[2026-06-08T08:49:18] 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=5321927)
[2026-06-08T08:49:21] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5321927)
[2026-06-08T08:49:24] Filtering viral contigs with expression lower than the top 5 (remaining=5321927)
[2026-06-08T08:49:31] Filtering viral contigs with less than 5% coverage (remaining=5321927)
[2026-06-08T08:49:34] Estimating fragment length (mate gap mean=-83.6033, mate gap stddev=32.3332, read length mean=136.296)
[2026-06-08T08:49:34] Filtering read-through fragments with a distance <=10000bp (remaining=5083421)
[2026-06-08T08:49:37] Filtering inconsistently clipped mates (remaining=5017239)
[2026-06-08T08:49:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4883513)
[2026-06-08T08:49:44] Filtering fragments with small insert size (remaining=4882845)
[2026-06-08T08:49:47] Filtering alignments with long gaps (remaining=4882845)
[2026-06-08T08:49:50] Filtering fragments with both mates in the same gene (remaining=4882088)
[2026-06-08T08:49:53] Filtering fusions arising from hairpin structures (remaining=4640256)
[2026-06-08T08:49:56] Filtering reads with a mismatch p-value <=0.01 (remaining=2273366)
[2026-06-08T08:50:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=639518)
[2026-06-08T08:50:24] Finding fusions and counting supporting reads (total=501166)
[2026-06-08T08:50:50] Merging adjacent fusion breakpoints (remaining=497616)
[2026-06-08T08:50:52] Filtering multi-mapping fusions by alignment score and read support (remaining=338753)
[2026-06-08T08:51:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:51:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=336118)
[2026-06-08T08:51:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=177012)
[2026-06-08T08:51:58] Filtering fusions with <2 supporting reads (remaining=32897)
[2026-06-08T08:51:59] Filtering fusions with an e-value >=0.3 (remaining=17315)
[2026-06-08T08:52:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=17348)
[2026-06-08T08:52:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=17287)
[2026-06-08T08:52:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=17287)
[2026-06-08T08:52:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5969)
[2026-06-08T08:52:17] Searching for fusions with spliced split reads (remaining=6090)
[2026-06-08T08:52:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=3429)
[2026-06-08T08:52:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3373)
[2026-06-08T08:52:27] Searching for fusions with >=4 spliced events (remaining=3962)
[2026-06-08T08:52:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1328)
[2026-06-08T08:52:51] Filtering fusions with anchors <=23nt (remaining=1024)
[2026-06-08T08:52:52] Filtering end-to-end fusions with low support (remaining=992)
[2026-06-08T08:52:53] Filtering fusions with no coverage around the breakpoints (remaining=963)
[2026-06-08T08:52:54] Indexing gene sequences 
[2026-06-08T08:53:01] Filtering genes with >=30% identity (remaining=285)
[2026-06-08T08:53:05] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=146)
[2026-06-08T08:53:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=143)
[2026-06-08T08:53:11] Searching for additional isoforms (remaining=178)
[2026-06-08T08:53:13] Assigning confidence scores to events 
[2026-06-08T08:53:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:53:18] Writing fusions to file 'tih_rna_sample_00592_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:53:20] Writing discarded fusions to file 'tih_rna_sample_00592_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:54:09] Freeing resources
[2026-06-08T08:54:45] Done (elapsed time=00:15:18, CPU time=00:15:17, peak memory=14.4gb)