[2026-06-03T20:51:42] Launching Arriba 2.4.0
[2026-06-03T20:51:42] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:51:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:51:59] Reading chimeric alignments from 'aih-tih-sc-64fc89-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10790840)
[2026-06-03T20:59:51] Marking multi-mapping alignments (marked=7202334)
[2026-06-03T20:59:55] Detecting strandedness (reverse)
[2026-06-03T20:59:55] Assigning strands to alignments 
[2026-06-03T20:59:57] Annotating alignments 
[2026-06-03T21:00:28] Filtering duplicates (remaining=7196003)
[2026-06-03T21:00:35] 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=6671108)
[2026-06-03T21:00:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6671108)
[2026-06-03T21:00:39] Filtering viral contigs with expression lower than the top 5 (remaining=6671108)
[2026-06-03T21:00:43] Filtering viral contigs with less than 5% coverage (remaining=6671108)
[2026-06-03T21:00:45] Estimating fragment length (mate gap mean=-86.5123, mate gap stddev=28.226, read length mean=128.799)
[2026-06-03T21:00:45] Filtering read-through fragments with a distance <=10000bp (remaining=6256895)
[2026-06-03T21:00:47] Filtering inconsistently clipped mates (remaining=6123150)
[2026-06-03T21:00:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5964964)
[2026-06-03T21:00:54] Filtering fragments with small insert size (remaining=5963932)
[2026-06-03T21:00:56] Filtering alignments with long gaps (remaining=5963932)
[2026-06-03T21:00:58] Filtering fragments with both mates in the same gene (remaining=5962855)
[2026-06-03T21:01:00] Filtering fusions arising from hairpin structures (remaining=5539685)
[2026-06-03T21:01:02] Filtering reads with a mismatch p-value <=0.01 (remaining=2406384)
[2026-06-03T21:01:16] Filtering reads with low entropy (k-mer content >=60%) (remaining=1289689)
[2026-06-03T21:01:28] Finding fusions and counting supporting reads (total=980051)
[2026-06-03T21:01:44] Merging adjacent fusion breakpoints (remaining=968083)
[2026-06-03T21:01:46] Filtering multi-mapping fusions by alignment score and read support (remaining=593962)
[2026-06-03T21:02:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T21:02:27] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=592024)
[2026-06-03T21:02:28] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=355516)
[2026-06-03T21:02:29] Filtering fusions with <2 supporting reads (remaining=36746)
[2026-06-03T21:02:30] Filtering fusions with an e-value >=0.3 (remaining=7945)
[2026-06-03T21:02:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8001)
[2026-06-03T21:02:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7914)
[2026-06-03T21:02:34] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7914)
[2026-06-03T21:02:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7667)
[2026-06-03T21:02:41] Searching for fusions with spliced split reads (remaining=7772)
[2026-06-03T21:02:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=4899)
[2026-06-03T21:02:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4854)
[2026-06-03T21:02:48] Searching for fusions with >=4 spliced events (remaining=6473)
[2026-06-03T21:02:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3046)
[2026-06-03T21:03:08] Filtering fusions with anchors <=23nt (remaining=2591)
[2026-06-03T21:03:09] Filtering end-to-end fusions with low support (remaining=2528)
[2026-06-03T21:03:09] Filtering fusions with no coverage around the breakpoints (remaining=2501)
[2026-06-03T21:03:10] Indexing gene sequences 
[2026-06-03T21:03:17] Filtering genes with >=30% identity (remaining=1277)
[2026-06-03T21:03:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=973)
[2026-06-03T21:03:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=520)
[2026-06-03T21:03:46] Searching for additional isoforms (remaining=1101)
[2026-06-03T21:03:47] Assigning confidence scores to events 
[2026-06-03T21:03:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T21:03:51] Writing fusions to file 'aih-tih-sc-64fc89-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T21:03:59] Writing discarded fusions to file 'aih-tih-sc-64fc89-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T21:04:32] Freeing resources
[2026-06-03T21:04:50] Done (elapsed time=00:13:08, CPU time=00:13:07, peak memory=15.9gb)