[2026-06-08T08:46:28] Launching Arriba 2.4.0
[2026-06-08T08:46:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:46:47] Reading chimeric alignments from 'aih-tih-sc-488877-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10470916)
[2026-06-08T08:54:42] Marking multi-mapping alignments (marked=6415290)
[2026-06-08T08:54:47] Detecting strandedness (reverse)
[2026-06-08T08:54:47] Assigning strands to alignments 
[2026-06-08T08:54:49] Annotating alignments 
[2026-06-08T08:55:26] Filtering duplicates (remaining=5979961)
[2026-06-08T08:55:34] 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=5751358)
[2026-06-08T08:55:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5751358)
[2026-06-08T08:55:38] Filtering viral contigs with expression lower than the top 5 (remaining=5751358)
[2026-06-08T08:55:43] Filtering viral contigs with less than 5% coverage (remaining=5751358)
[2026-06-08T08:55:46] Estimating fragment length (mate gap mean=-86.5711, mate gap stddev=28.8679, read length mean=133.054)
[2026-06-08T08:55:46] Filtering read-through fragments with a distance <=10000bp (remaining=5422640)
[2026-06-08T08:55:48] Filtering inconsistently clipped mates (remaining=5333305)
[2026-06-08T08:55:51] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5212156)
[2026-06-08T08:55:55] Filtering fragments with small insert size (remaining=5211516)
[2026-06-08T08:55:58] Filtering alignments with long gaps (remaining=5211516)
[2026-06-08T08:56:00] Filtering fragments with both mates in the same gene (remaining=5210399)
[2026-06-08T08:56:03] Filtering fusions arising from hairpin structures (remaining=4907112)
[2026-06-08T08:56:06] Filtering reads with a mismatch p-value <=0.01 (remaining=2392364)
[2026-06-08T08:56:19] Filtering reads with low entropy (k-mer content >=60%) (remaining=1027987)
[2026-06-08T08:56:30] Finding fusions and counting supporting reads (total=753381)
[2026-06-08T08:56:49] Merging adjacent fusion breakpoints (remaining=747026)
[2026-06-08T08:56:51] Filtering multi-mapping fusions by alignment score and read support (remaining=482951)
[2026-06-08T08:57:26] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:33] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=479854)
[2026-06-08T08:57:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=265529)
[2026-06-08T08:57:35] Filtering fusions with <2 supporting reads (remaining=47292)
[2026-06-08T08:57:36] Filtering fusions with an e-value >=0.3 (remaining=18971)
[2026-06-08T08:57:37] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=19019)
[2026-06-08T08:57:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=18937)
[2026-06-08T08:57:41] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=18937)
[2026-06-08T08:57:43] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8769)
[2026-06-08T08:57:48] Searching for fusions with spliced split reads (remaining=8911)
[2026-06-08T08:57:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=5334)
[2026-06-08T08:57:54] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5272)
[2026-06-08T08:57:54] Searching for fusions with >=4 spliced events (remaining=6478)
[2026-06-08T08:57:56] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2055)
[2026-06-08T08:58:11] Filtering fusions with anchors <=23nt (remaining=1744)
[2026-06-08T08:58:12] Filtering end-to-end fusions with low support (remaining=1700)
[2026-06-08T08:58:12] Filtering fusions with no coverage around the breakpoints (remaining=1663)
[2026-06-08T08:58:13] Indexing gene sequences 
[2026-06-08T08:58:19] Filtering genes with >=30% identity (remaining=490)
[2026-06-08T08:58:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=255)
[2026-06-08T08:58:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=206)
[2026-06-08T08:58:30] Searching for additional isoforms (remaining=249)
[2026-06-08T08:58:31] Assigning confidence scores to events 
[2026-06-08T08:58:34] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:34] Writing fusions to file 'aih-tih-sc-488877-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:58:36] Writing discarded fusions to file 'aih-tih-sc-488877-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:07] Freeing resources
[2026-06-08T08:59:26] Done (elapsed time=00:12:58, CPU time=00:12:57, peak memory=15gb)