[2026-06-03T20:37:46] Launching Arriba 2.4.0
[2026-06-03T20:37:46] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:37:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:37:57] Reading chimeric alignments from 'aih-tih-sc-a51633-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=12600400)
[2026-06-03T20:45:07] Marking multi-mapping alignments (marked=8657519)
[2026-06-03T20:45:12] Detecting strandedness (reverse)
[2026-06-03T20:45:12] Assigning strands to alignments 
[2026-06-03T20:45:15] Annotating alignments 
[2026-06-03T20:45:52] Filtering duplicates (remaining=8116908)
[2026-06-03T20:46:00] 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=7261777)
[2026-06-03T20:46:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7261777)
[2026-06-03T20:46:05] Filtering viral contigs with expression lower than the top 5 (remaining=7261777)
[2026-06-03T20:46:10] Filtering viral contigs with less than 5% coverage (remaining=7261777)
[2026-06-03T20:46:13] Estimating fragment length (mate gap mean=-82.8109, mate gap stddev=32.0062, read length mean=132.438)
[2026-06-03T20:46:13] Filtering read-through fragments with a distance <=10000bp (remaining=6847830)
[2026-06-03T20:46:16] Filtering inconsistently clipped mates (remaining=6711096)
[2026-06-03T20:46:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6495003)
[2026-06-03T20:46:23] Filtering fragments with small insert size (remaining=6494073)
[2026-06-03T20:46:26] Filtering alignments with long gaps (remaining=6494073)
[2026-06-03T20:46:29] Filtering fragments with both mates in the same gene (remaining=6492757)
[2026-06-03T20:46:31] Filtering fusions arising from hairpin structures (remaining=6035860)
[2026-06-03T20:46:34] Filtering reads with a mismatch p-value <=0.01 (remaining=2760319)
[2026-06-03T20:46:50] Filtering reads with low entropy (k-mer content >=60%) (remaining=1253954)
[2026-06-03T20:47:05] Finding fusions and counting supporting reads (total=990805)
[2026-06-03T20:47:24] Merging adjacent fusion breakpoints (remaining=982754)
[2026-06-03T20:47:26] Filtering multi-mapping fusions by alignment score and read support (remaining=603226)
[2026-06-03T20:48:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:48:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=599201)
[2026-06-03T20:48:11] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=386103)
[2026-06-03T20:48:13] Filtering fusions with <2 supporting reads (remaining=43826)
[2026-06-03T20:48:14] Filtering fusions with an e-value >=0.3 (remaining=16995)
[2026-06-03T20:48:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=17068)
[2026-06-03T20:48:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=16984)
[2026-06-03T20:48:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=16984)
[2026-06-03T20:48:22] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8978)
[2026-06-03T20:48:28] Searching for fusions with spliced split reads (remaining=9000)
[2026-06-03T20:48:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=4079)
[2026-06-03T20:48:36] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4033)
[2026-06-03T20:48:37] Searching for fusions with >=4 spliced events (remaining=4974)
[2026-06-03T20:48:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2036)
[2026-06-03T20:48:53] Filtering fusions with anchors <=23nt (remaining=1608)
[2026-06-03T20:48:54] Filtering end-to-end fusions with low support (remaining=1563)
[2026-06-03T20:48:55] Filtering fusions with no coverage around the breakpoints (remaining=1531)
[2026-06-03T20:48:56] Indexing gene sequences 
[2026-06-03T20:49:02] Filtering genes with >=30% identity (remaining=536)
[2026-06-03T20:49:06] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=333)
[2026-06-03T20:49:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=242)
[2026-06-03T20:49:15] Searching for additional isoforms (remaining=359)
[2026-06-03T20:49:17] Assigning confidence scores to events 
[2026-06-03T20:49:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:49:21] Writing fusions to file 'aih-tih-sc-a51633-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:49:24] Writing discarded fusions to file 'aih-tih-sc-a51633-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:49:55] Freeing resources
[2026-06-03T20:50:16] Done (elapsed time=00:12:30, CPU time=00:12:29, peak memory=17.7gb)