[2026-06-08T08:45:59] Launching Arriba 2.4.0
[2026-06-08T08:45:59] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:09] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:46:13] Reading chimeric alignments from 'tih_rna_sample_00146_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9684265)
[2026-06-08T08:53:28] Marking multi-mapping alignments (marked=5891000)
[2026-06-08T08:53:32] Detecting strandedness (reverse)
[2026-06-08T08:53:32] Assigning strands to alignments 
[2026-06-08T08:53:34] Annotating alignments 
[2026-06-08T08:54:08] Filtering duplicates (remaining=4853982)
[2026-06-08T08:54:14] 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=4662354)
[2026-06-08T08:54:16] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4662354)
[2026-06-08T08:54:18] Filtering viral contigs with expression lower than the top 5 (remaining=4662354)
[2026-06-08T08:54:22] Filtering viral contigs with less than 5% coverage (remaining=4662354)
[2026-06-08T08:54:24] Estimating fragment length (mate gap mean=-86.9942, mate gap stddev=31.4502, read length mean=138.526)
[2026-06-08T08:54:25] Filtering read-through fragments with a distance <=10000bp (remaining=4378492)
[2026-06-08T08:54:26] Filtering inconsistently clipped mates (remaining=4319122)
[2026-06-08T08:54:28] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4183167)
[2026-06-08T08:54:32] Filtering fragments with small insert size (remaining=4182677)
[2026-06-08T08:54:34] Filtering alignments with long gaps (remaining=4182677)
[2026-06-08T08:54:36] Filtering fragments with both mates in the same gene (remaining=4181783)
[2026-06-08T08:54:38] Filtering fusions arising from hairpin structures (remaining=3976662)
[2026-06-08T08:54:40] Filtering reads with a mismatch p-value <=0.01 (remaining=1738876)
[2026-06-08T08:54:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=713907)
[2026-06-08T08:55:00] Finding fusions and counting supporting reads (total=552705)
[2026-06-08T08:55:16] Merging adjacent fusion breakpoints (remaining=548317)
[2026-06-08T08:55:17] Filtering multi-mapping fusions by alignment score and read support (remaining=363295)
[2026-06-08T08:55:50] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:55:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=359425)
[2026-06-08T08:55:56] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=188217)
[2026-06-08T08:55:57] Filtering fusions with <2 supporting reads (remaining=28310)
[2026-06-08T08:55:58] Filtering fusions with an e-value >=0.3 (remaining=10943)
[2026-06-08T08:55:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10980)
[2026-06-08T08:56:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10918)
[2026-06-08T08:56:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10918)
[2026-06-08T08:56:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6107)
[2026-06-08T08:56:08] Searching for fusions with spliced split reads (remaining=6253)
[2026-06-08T08:56:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=3794)
[2026-06-08T08:56:14] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3735)
[2026-06-08T08:56:14] Searching for fusions with >=4 spliced events (remaining=4263)
[2026-06-08T08:56:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1487)
[2026-06-08T08:56:30] Filtering fusions with anchors <=23nt (remaining=1149)
[2026-06-08T08:56:31] Filtering end-to-end fusions with low support (remaining=1102)
[2026-06-08T08:56:31] Filtering fusions with no coverage around the breakpoints (remaining=1064)
[2026-06-08T08:56:32] Indexing gene sequences 
[2026-06-08T08:56:36] Filtering genes with >=30% identity (remaining=361)
[2026-06-08T08:56:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=195)
[2026-06-08T08:56:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=182)
[2026-06-08T08:56:44] Searching for additional isoforms (remaining=264)
[2026-06-08T08:56:45] Assigning confidence scores to events 
[2026-06-08T08:56:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:56:48] Writing fusions to file 'tih_rna_sample_00146_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:56:50] Writing discarded fusions to file 'tih_rna_sample_00146_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:57:15] Freeing resources
[2026-06-08T08:57:31] Done (elapsed time=00:11:32, CPU time=00:11:31, peak memory=14.2gb)