[2026-06-08T08:46:30] Launching Arriba 2.4.0
[2026-06-08T08:46:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:46:49] Reading chimeric alignments from 'aih-tih-sc-7f9674-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9469775)
[2026-06-08T08:54:52] Marking multi-mapping alignments (marked=5946385)
[2026-06-08T08:54:56] Detecting strandedness (reverse)
[2026-06-08T08:54:56] Assigning strands to alignments 
[2026-06-08T08:54:58] Annotating alignments 
[2026-06-08T08:55:32] Filtering duplicates (remaining=6434574)
[2026-06-08T08:55:40] 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=6083080)
[2026-06-08T08:55:42] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6083080)
[2026-06-08T08:55:44] Filtering viral contigs with expression lower than the top 5 (remaining=6083080)
[2026-06-08T08:55:48] Filtering viral contigs with less than 5% coverage (remaining=6083080)
[2026-06-08T08:55:51] Estimating fragment length (mate gap mean=-84.137, mate gap stddev=29.4082, read length mean=128.02)
[2026-06-08T08:55:51] Filtering read-through fragments with a distance <=10000bp (remaining=5692723)
[2026-06-08T08:55:53] Filtering inconsistently clipped mates (remaining=5569006)
[2026-06-08T08:55:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5418495)
[2026-06-08T08:56:00] Filtering fragments with small insert size (remaining=5417334)
[2026-06-08T08:56:02] Filtering alignments with long gaps (remaining=5417334)
[2026-06-08T08:56:04] Filtering fragments with both mates in the same gene (remaining=5416010)
[2026-06-08T08:56:06] Filtering fusions arising from hairpin structures (remaining=5016380)
[2026-06-08T08:56:09] Filtering reads with a mismatch p-value <=0.01 (remaining=2268718)
[2026-06-08T08:56:22] Filtering reads with low entropy (k-mer content >=60%) (remaining=1153531)
[2026-06-08T08:56:34] Finding fusions and counting supporting reads (total=866742)
[2026-06-08T08:56:51] Merging adjacent fusion breakpoints (remaining=857980)
[2026-06-08T08:56:53] Filtering multi-mapping fusions by alignment score and read support (remaining=571876)
[2026-06-08T08:57:25] 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=569743)
[2026-06-08T08:57:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=338392)
[2026-06-08T08:57:35] Filtering fusions with <2 supporting reads (remaining=37795)
[2026-06-08T08:57:36] Filtering fusions with an e-value >=0.3 (remaining=9667)
[2026-06-08T08:57:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9735)
[2026-06-08T08:57:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9656)
[2026-06-08T08:57:41] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9656)
[2026-06-08T08:57:43] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7988)
[2026-06-08T08:57:48] Searching for fusions with spliced split reads (remaining=8006)
[2026-06-08T08:57:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=4884)
[2026-06-08T08:57:54] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4829)
[2026-06-08T08:57:55] Searching for fusions with >=4 spliced events (remaining=5814)
[2026-06-08T08:57:56] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1914)
[2026-06-08T08:58:12] Filtering fusions with anchors <=23nt (remaining=1595)
[2026-06-08T08:58:13] Filtering end-to-end fusions with low support (remaining=1550)
[2026-06-08T08:58:14] Filtering fusions with no coverage around the breakpoints (remaining=1518)
[2026-06-08T08:58:14] Indexing gene sequences 
[2026-06-08T08:58:19] Filtering genes with >=30% identity (remaining=445)
[2026-06-08T08:58:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=207)
[2026-06-08T08:58:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=204)
[2026-06-08T08:58:30] Searching for additional isoforms (remaining=233)
[2026-06-08T08:58:31] Assigning confidence scores to events 
[2026-06-08T08:58:35] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:35] Writing fusions to file 'aih-tih-sc-7f9674-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:58:37] Writing discarded fusions to file 'aih-tih-sc-7f9674-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:09] Freeing resources
[2026-06-08T08:59:27] Done (elapsed time=00:12:57, CPU time=00:12:54, peak memory=14.2gb)