[2026-06-08T09:54:32] Launching Arriba 2.4.0
[2026-06-08T09:54:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:54:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:54:45] Reading chimeric alignments from 'tih_rna_sample_00725_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=13574221)
[2026-06-08T10:01:42] Marking multi-mapping alignments (marked=8677423)
[2026-06-08T10:01:47] Detecting strandedness (reverse)
[2026-06-08T10:01:47] Assigning strands to alignments 
[2026-06-08T10:01:50] Annotating alignments 
[2026-06-08T10:02:31] Filtering duplicates (remaining=7176437)
[2026-06-08T10:02:39] 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=6725811)
[2026-06-08T10:02:42] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6725811)
[2026-06-08T10:02:44] Filtering viral contigs with expression lower than the top 5 (remaining=6725811)
[2026-06-08T10:02:50] Filtering viral contigs with less than 5% coverage (remaining=6725811)
[2026-06-08T10:02:53] Estimating fragment length (mate gap mean=-88.0371, mate gap stddev=29.9019, read length mean=131.007)
[2026-06-08T10:02:53] Filtering read-through fragments with a distance <=10000bp (remaining=6339325)
[2026-06-08T10:02:56] Filtering inconsistently clipped mates (remaining=6245052)
[2026-06-08T10:02:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6117456)
[2026-06-08T10:03:03] Filtering fragments with small insert size (remaining=6116570)
[2026-06-08T10:03:05] Filtering alignments with long gaps (remaining=6116570)
[2026-06-08T10:03:08] Filtering fragments with both mates in the same gene (remaining=6115518)
[2026-06-08T10:03:11] Filtering fusions arising from hairpin structures (remaining=5823827)
[2026-06-08T10:03:14] Filtering reads with a mismatch p-value <=0.01 (remaining=2599747)
[2026-06-08T10:03:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=910195)
[2026-06-08T10:03:39] Finding fusions and counting supporting reads (total=723537)
[2026-06-08T10:04:00] Merging adjacent fusion breakpoints (remaining=712553)
[2026-06-08T10:04:02] Filtering multi-mapping fusions by alignment score and read support (remaining=456906)
[2026-06-08T10:04:43] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T10:04:51] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=454536)
[2026-06-08T10:04:52] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=239793)
[2026-06-08T10:04:53] Filtering fusions with <2 supporting reads (remaining=45777)
[2026-06-08T10:04:55] Filtering fusions with an e-value >=0.3 (remaining=22435)
[2026-06-08T10:04:56] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=22480)
[2026-06-08T10:05:00] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=22325)
[2026-06-08T10:05:01] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=22329)
[2026-06-08T10:05:03] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8218)
[2026-06-08T10:05:09] Searching for fusions with spliced split reads (remaining=8319)
[2026-06-08T10:05:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=5257)
[2026-06-08T10:05:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5198)
[2026-06-08T10:05:18] Searching for fusions with >=4 spliced events (remaining=5937)
[2026-06-08T10:05:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2213)
[2026-06-08T10:05:52] Filtering fusions with anchors <=23nt (remaining=1309)
[2026-06-08T10:05:53] Filtering end-to-end fusions with low support (remaining=1255)
[2026-06-08T10:05:54] Filtering fusions with no coverage around the breakpoints (remaining=1220)
[2026-06-08T10:05:54] Indexing gene sequences 
[2026-06-08T10:06:00] Filtering genes with >=30% identity (remaining=375)
[2026-06-08T10:06:02] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=197)
[2026-06-08T10:06:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=192)
[2026-06-08T10:06:07] Searching for additional isoforms (remaining=220)
[2026-06-08T10:06:09] Assigning confidence scores to events 
[2026-06-08T10:06:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T10:06:13] Writing fusions to file 'tih_rna_sample_00725_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T10:06:15] Writing discarded fusions to file 'tih_rna_sample_00725_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T10:06:43] Freeing resources
[2026-06-08T10:07:04] Done (elapsed time=00:12:32, CPU time=00:12:31, peak memory=18.3gb)