[2026-06-03T20:00:34] Launching Arriba 2.4.0
[2026-06-03T20:00:34] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:00:52] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:01:00] Reading chimeric alignments from 'aih-tih-sc-c35cc3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10129626)
[2026-06-03T20:11:46] Marking multi-mapping alignments (marked=6880235)
[2026-06-03T20:11:51] Detecting strandedness (reverse)
[2026-06-03T20:11:51] Assigning strands to alignments 
[2026-06-03T20:11:53] Annotating alignments 
[2026-06-03T20:12:37] Filtering duplicates (remaining=5124253)
[2026-06-03T20:12:45] 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=4761536)
[2026-06-03T20:12:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4761536)
[2026-06-03T20:12:49] Filtering viral contigs with expression lower than the top 5 (remaining=4761536)
[2026-06-03T20:12:55] Filtering viral contigs with less than 5% coverage (remaining=4761536)
[2026-06-03T20:12:57] Estimating fragment length (mate gap mean=-84.5204, mate gap stddev=27.7546, read length mean=121.76)
[2026-06-03T20:12:58] Filtering read-through fragments with a distance <=10000bp (remaining=4453631)
[2026-06-03T20:13:00] Filtering inconsistently clipped mates (remaining=4343331)
[2026-06-03T20:13:02] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4183050)
[2026-06-03T20:13:07] Filtering fragments with small insert size (remaining=4181944)
[2026-06-03T20:13:09] Filtering alignments with long gaps (remaining=4181944)
[2026-06-03T20:13:11] Filtering fragments with both mates in the same gene (remaining=4181095)
[2026-06-03T20:13:13] Filtering fusions arising from hairpin structures (remaining=3903955)
[2026-06-03T20:13:16] Filtering reads with a mismatch p-value <=0.01 (remaining=1498136)
[2026-06-03T20:13:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=734464)
[2026-06-03T20:13:36] Finding fusions and counting supporting reads (total=616254)
[2026-06-03T20:13:56] Merging adjacent fusion breakpoints (remaining=609820)
[2026-06-03T20:13:57] Filtering multi-mapping fusions by alignment score and read support (remaining=352007)
[2026-06-03T20:14:35] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:14:43] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=350712)
[2026-06-03T20:14:44] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=198850)
[2026-06-03T20:14:45] Filtering fusions with <2 supporting reads (remaining=20511)
[2026-06-03T20:14:45] Filtering fusions with an e-value >=0.3 (remaining=4989)
[2026-06-03T20:14:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5036)
[2026-06-03T20:14:50] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4956)
[2026-06-03T20:14:50] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4957)
[2026-06-03T20:14:52] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4876)
[2026-06-03T20:14:57] Searching for fusions with spliced split reads (remaining=4942)
[2026-06-03T20:15:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=3490)
[2026-06-03T20:15:04] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3454)
[2026-06-03T20:15:05] Searching for fusions with >=4 spliced events (remaining=3991)
[2026-06-03T20:15:06] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1728)
[2026-06-03T20:15:29] Filtering fusions with anchors <=23nt (remaining=1328)
[2026-06-03T20:15:30] Filtering end-to-end fusions with low support (remaining=1287)
[2026-06-03T20:15:30] Filtering fusions with no coverage around the breakpoints (remaining=1259)
[2026-06-03T20:15:31] Indexing gene sequences 
[2026-06-03T20:15:38] Filtering genes with >=30% identity (remaining=385)
[2026-06-03T20:15:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=148)
[2026-06-03T20:15:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=148)
[2026-06-03T20:15:44] Searching for additional isoforms (remaining=186)
[2026-06-03T20:15:45] Assigning confidence scores to events 
[2026-06-03T20:15:49] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:15:49] Writing fusions to file 'aih-tih-sc-c35cc3-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:15:51] Writing discarded fusions to file 'aih-tih-sc-c35cc3-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:16:26] Freeing resources
[2026-06-03T20:16:46] Done (elapsed time=00:16:12, CPU time=00:16:10, peak memory=14.9gb)