[2026-06-03T20:14:59] Launching Arriba 2.4.0
[2026-06-03T20:14:59] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:15:07] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:15:11] Reading chimeric alignments from 'aih-tih-sc-538ae3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10195403)
[2026-06-03T20:22:06] Marking multi-mapping alignments (marked=6896908)
[2026-06-03T20:22:10] Detecting strandedness (reverse)
[2026-06-03T20:22:10] Assigning strands to alignments 
[2026-06-03T20:22:12] Annotating alignments 
[2026-06-03T20:22:42] Filtering duplicates (remaining=7123111)
[2026-06-03T20:22:49] 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=6705797)
[2026-06-03T20:22:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6705797)
[2026-06-03T20:22:52] Filtering viral contigs with expression lower than the top 5 (remaining=6705797)
[2026-06-03T20:22:57] Filtering viral contigs with less than 5% coverage (remaining=6705797)
[2026-06-03T20:22:59] Estimating fragment length (mate gap mean=-85.04, mate gap stddev=29.1752, read length mean=128.69)
[2026-06-03T20:22:59] Filtering read-through fragments with a distance <=10000bp (remaining=6181379)
[2026-06-03T20:23:01] Filtering inconsistently clipped mates (remaining=6060108)
[2026-06-03T20:23:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5896592)
[2026-06-03T20:23:08] Filtering fragments with small insert size (remaining=5895691)
[2026-06-03T20:23:10] Filtering alignments with long gaps (remaining=5895691)
[2026-06-03T20:23:12] Filtering fragments with both mates in the same gene (remaining=5894595)
[2026-06-03T20:23:14] Filtering fusions arising from hairpin structures (remaining=5468322)
[2026-06-03T20:23:16] Filtering reads with a mismatch p-value <=0.01 (remaining=2448477)
[2026-06-03T20:23:30] Filtering reads with low entropy (k-mer content >=60%) (remaining=1246555)
[2026-06-03T20:23:40] Finding fusions and counting supporting reads (total=954628)
[2026-06-03T20:23:57] Merging adjacent fusion breakpoints (remaining=942044)
[2026-06-03T20:23:58] Filtering multi-mapping fusions by alignment score and read support (remaining=567973)
[2026-06-03T20:24:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:24:37] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=565935)
[2026-06-03T20:24:38] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=328220)
[2026-06-03T20:24:39] Filtering fusions with <2 supporting reads (remaining=34986)
[2026-06-03T20:24:40] Filtering fusions with an e-value >=0.3 (remaining=9646)
[2026-06-03T20:24:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9705)
[2026-06-03T20:24:44] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9550)
[2026-06-03T20:24:45] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9550)
[2026-06-03T20:24:47] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8074)
[2026-06-03T20:24:52] Searching for fusions with spliced split reads (remaining=8102)
[2026-06-03T20:24:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=4701)
[2026-06-03T20:24:59] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4649)
[2026-06-03T20:24:59] Searching for fusions with >=4 spliced events (remaining=5676)
[2026-06-03T20:25:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2488)
[2026-06-03T20:25:18] Filtering fusions with anchors <=23nt (remaining=1886)
[2026-06-03T20:25:19] Filtering end-to-end fusions with low support (remaining=1826)
[2026-06-03T20:25:20] Filtering fusions with no coverage around the breakpoints (remaining=1793)
[2026-06-03T20:25:20] Indexing gene sequences 
[2026-06-03T20:25:27] Filtering genes with >=30% identity (remaining=538)
[2026-06-03T20:25:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=212)
[2026-06-03T20:25:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=205)
[2026-06-03T20:25:34] Searching for additional isoforms (remaining=253)
[2026-06-03T20:25:35] Assigning confidence scores to events 
[2026-06-03T20:25:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:25:39] Writing fusions to file 'aih-tih-sc-538ae3-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:25:41] Writing discarded fusions to file 'aih-tih-sc-538ae3-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:26:10] Freeing resources
[2026-06-03T20:26:26] Done (elapsed time=00:11:27, CPU time=00:11:26, peak memory=15.1gb)