[2026-06-08T08:37:31] Launching Arriba 2.4.0
[2026-06-08T08:37:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:37:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:37:43] Reading chimeric alignments from 'aih-tih-sc-f26674-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10136924)
[2026-06-08T08:44:19] Marking multi-mapping alignments (marked=6320962)
[2026-06-08T08:44:22] Detecting strandedness (reverse)
[2026-06-08T08:44:22] Assigning strands to alignments 
[2026-06-08T08:44:24] Annotating alignments 
[2026-06-08T08:44:55] Filtering duplicates (remaining=7110885)
[2026-06-08T08:45:02] 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=6751567)
[2026-06-08T08:45:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6751567)
[2026-06-08T08:45:05] Filtering viral contigs with expression lower than the top 5 (remaining=6751567)
[2026-06-08T08:45:10] Filtering viral contigs with less than 5% coverage (remaining=6751567)
[2026-06-08T08:45:12] Estimating fragment length (mate gap mean=-85.8545, mate gap stddev=28.562, read length mean=129.353)
[2026-06-08T08:45:12] Filtering read-through fragments with a distance <=10000bp (remaining=6298976)
[2026-06-08T08:45:14] Filtering inconsistently clipped mates (remaining=6170147)
[2026-06-08T08:45:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6012759)
[2026-06-08T08:45:20] Filtering fragments with small insert size (remaining=6011556)
[2026-06-08T08:45:22] Filtering alignments with long gaps (remaining=6011555)
[2026-06-08T08:45:24] Filtering fragments with both mates in the same gene (remaining=6010446)
[2026-06-08T08:45:27] Filtering fusions arising from hairpin structures (remaining=5609684)
[2026-06-08T08:45:29] Filtering reads with a mismatch p-value <=0.01 (remaining=2580645)
[2026-06-08T08:45:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=1348163)
[2026-06-08T08:45:54] Finding fusions and counting supporting reads (total=1054301)
[2026-06-08T08:46:10] Merging adjacent fusion breakpoints (remaining=1047112)
[2026-06-08T08:46:12] Filtering multi-mapping fusions by alignment score and read support (remaining=697196)
[2026-06-08T08:46:43] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:46:51] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=695427)
[2026-06-08T08:46:52] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=439914)
[2026-06-08T08:46:54] Filtering fusions with <2 supporting reads (remaining=39543)
[2026-06-08T08:46:54] Filtering fusions with an e-value >=0.3 (remaining=8548)
[2026-06-08T08:46:55] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8608)
[2026-06-08T08:46:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8558)
[2026-06-08T08:47:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8558)
[2026-06-08T08:47:02] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7079)
[2026-06-08T08:47:07] Searching for fusions with spliced split reads (remaining=7206)
[2026-06-08T08:47:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=4646)
[2026-06-08T08:47:14] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4562)
[2026-06-08T08:47:14] Searching for fusions with >=4 spliced events (remaining=5617)
[2026-06-08T08:47:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2265)
[2026-06-08T08:47:31] Filtering fusions with anchors <=23nt (remaining=1883)
[2026-06-08T08:47:32] Filtering end-to-end fusions with low support (remaining=1843)
[2026-06-08T08:47:33] Filtering fusions with no coverage around the breakpoints (remaining=1810)
[2026-06-08T08:47:34] Indexing gene sequences 
[2026-06-08T08:47:41] Filtering genes with >=30% identity (remaining=529)
[2026-06-08T08:47:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=221)
[2026-06-08T08:47:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=209)
[2026-06-08T08:47:50] Searching for additional isoforms (remaining=277)
[2026-06-08T08:47:52] Assigning confidence scores to events 
[2026-06-08T08:47:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:56] Writing fusions to file 'aih-tih-sc-f26674-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:47:58] Writing discarded fusions to file 'aih-tih-sc-f26674-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:48:29] Freeing resources
[2026-06-08T08:48:45] Done (elapsed time=00:11:14, CPU time=00:11:13, peak memory=15gb)