[2026-06-08T08:44:51] Launching Arriba 2.4.0
[2026-06-08T08:44:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:45:01] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:45:05] Reading chimeric alignments from 'tih_rna_sample_00480_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10169997)
[2026-06-08T08:51:33] Marking multi-mapping alignments (marked=6818763)
[2026-06-08T08:51:38] Detecting strandedness (reverse)
[2026-06-08T08:51:38] Assigning strands to alignments 
[2026-06-08T08:51:40] Annotating alignments 
[2026-06-08T08:52:14] Filtering duplicates (remaining=4321148)
[2026-06-08T08:52:20] 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=4040231)
[2026-06-08T08:52:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4040231)
[2026-06-08T08:52:24] Filtering viral contigs with expression lower than the top 5 (remaining=4040231)
[2026-06-08T08:52:28] Filtering viral contigs with less than 5% coverage (remaining=4040231)
[2026-06-08T08:52:31] Estimating fragment length (mate gap mean=-87.3386, mate gap stddev=28.5007, read length mean=131.205)
[2026-06-08T08:52:31] Filtering read-through fragments with a distance <=10000bp (remaining=3838170)
[2026-06-08T08:52:33] Filtering inconsistently clipped mates (remaining=3773563)
[2026-06-08T08:52:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3643015)
[2026-06-08T08:52:38] Filtering fragments with small insert size (remaining=3642314)
[2026-06-08T08:52:40] Filtering alignments with long gaps (remaining=3642314)
[2026-06-08T08:52:42] Filtering fragments with both mates in the same gene (remaining=3641668)
[2026-06-08T08:52:44] Filtering fusions arising from hairpin structures (remaining=3464331)
[2026-06-08T08:52:47] Filtering reads with a mismatch p-value <=0.01 (remaining=1399310)
[2026-06-08T08:52:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=535551)
[2026-06-08T08:53:04] Finding fusions and counting supporting reads (total=443619)
[2026-06-08T08:53:19] Merging adjacent fusion breakpoints (remaining=440639)
[2026-06-08T08:53:20] Filtering multi-mapping fusions by alignment score and read support (remaining=260020)
[2026-06-08T08:53:53] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:53:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=258438)
[2026-06-08T08:53:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=147358)
[2026-06-08T08:54:00] Filtering fusions with <2 supporting reads (remaining=17211)
[2026-06-08T08:54:00] Filtering fusions with an e-value >=0.3 (remaining=4728)
[2026-06-08T08:54:01] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4757)
[2026-06-08T08:54:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4688)
[2026-06-08T08:54:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4688)
[2026-06-08T08:54:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4161)
[2026-06-08T08:54:10] Searching for fusions with spliced split reads (remaining=4272)
[2026-06-08T08:54:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=3020)
[2026-06-08T08:54:16] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2972)
[2026-06-08T08:54:16] Searching for fusions with >=4 spliced events (remaining=3459)
[2026-06-08T08:54:17] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1394)
[2026-06-08T08:54:30] Filtering fusions with anchors <=23nt (remaining=1185)
[2026-06-08T08:54:30] Filtering end-to-end fusions with low support (remaining=1155)
[2026-06-08T08:54:31] Filtering fusions with no coverage around the breakpoints (remaining=1113)
[2026-06-08T08:54:31] Indexing gene sequences 
[2026-06-08T08:54:38] Filtering genes with >=30% identity (remaining=480)
[2026-06-08T08:54:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=315)
[2026-06-08T08:54:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=219)
[2026-06-08T08:54:44] Searching for additional isoforms (remaining=312)
[2026-06-08T08:54:45] Assigning confidence scores to events 
[2026-06-08T08:54:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:54:48] Writing fusions to file 'tih_rna_sample_00480_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:54:50] Writing discarded fusions to file 'tih_rna_sample_00480_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:55:12] Freeing resources
[2026-06-08T08:55:28] Done (elapsed time=00:10:37, CPU time=00:10:36, peak memory=14.6gb)