[2026-06-08T09:06:34] Launching Arriba 2.4.0
[2026-06-08T09:06:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:06:43] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:06:47] Reading chimeric alignments from 'aih-tih-sc-a51633-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=12600400)
[2026-06-08T09:14:06] Marking multi-mapping alignments (marked=8657519)
[2026-06-08T09:14:12] Detecting strandedness (reverse)
[2026-06-08T09:14:12] Assigning strands to alignments 
[2026-06-08T09:14:15] Annotating alignments 
[2026-06-08T09:14:59] Filtering duplicates (remaining=8116908)
[2026-06-08T09:15:09] 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)
[2026-06-08T09:15:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7261777)
[2026-06-08T09:15:14] Filtering viral contigs with expression lower than the top 5 (remaining=7261777)
[2026-06-08T09:15:21] Filtering viral contigs with less than 5% coverage (remaining=7261777)
[2026-06-08T09:15:24] Estimating fragment length (mate gap mean=-82.8109, mate gap stddev=32.0062, read length mean=132.438)
[2026-06-08T09:15:24] Filtering read-through fragments with a distance <=10000bp (remaining=6847830)
[2026-06-08T09:15:27] Filtering inconsistently clipped mates (remaining=6711096)
[2026-06-08T09:15:30] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6495003)
[2026-06-08T09:15:36] Filtering fragments with small insert size (remaining=6494073)
[2026-06-08T09:15:39] Filtering alignments with long gaps (remaining=6494073)
[2026-06-08T09:15:42] Filtering fragments with both mates in the same gene (remaining=6492757)
[2026-06-08T09:15:45] Filtering fusions arising from hairpin structures (remaining=6035860)
[2026-06-08T09:15:49] Filtering reads with a mismatch p-value <=0.01 (remaining=2760319)
[2026-06-08T09:16:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=1253954)
[2026-06-08T09:16:19] Finding fusions and counting supporting reads (total=990805)
[2026-06-08T09:16:42] Merging adjacent fusion breakpoints (remaining=982754)
[2026-06-08T09:16:45] Filtering multi-mapping fusions by alignment score and read support (remaining=603226)
[2026-06-08T09:17:26] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:17:35] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=599201)
[2026-06-08T09:17:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=386103)
[2026-06-08T09:17:38] Filtering fusions with <2 supporting reads (remaining=43826)
[2026-06-08T09:17:39] Filtering fusions with an e-value >=0.3 (remaining=16995)
[2026-06-08T09:17:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=17068)
[2026-06-08T09:17:44] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=16984)
[2026-06-08T09:17:45] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=16984)
[2026-06-08T09:17:48] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8978)
[2026-06-08T09:17:54] Searching for fusions with spliced split reads (remaining=9000)
[2026-06-08T09:18:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=4079)
[2026-06-08T09:18:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4033)
[2026-06-08T09:18:03] Searching for fusions with >=4 spliced events (remaining=4974)
[2026-06-08T09:18:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2036)
[2026-06-08T09:18:20] Filtering fusions with anchors <=23nt (remaining=1608)
[2026-06-08T09:18:21] Filtering end-to-end fusions with low support (remaining=1563)
[2026-06-08T09:18:22] Filtering fusions with no coverage around the breakpoints (remaining=1531)
[2026-06-08T09:18:23] Indexing gene sequences 
[2026-06-08T09:18:29] Filtering genes with >=30% identity (remaining=536)
[2026-06-08T09:18:34] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=333)
[2026-06-08T09:18:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=242)
[2026-06-08T09:18:44] Searching for additional isoforms (remaining=359)
[2026-06-08T09:18:46] Assigning confidence scores to events 
[2026-06-08T09:18:50] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:18:50] Writing fusions to file 'aih-tih-sc-a51633-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:18:53] Writing discarded fusions to file 'aih-tih-sc-a51633-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:19:30] Freeing resources
[2026-06-08T09:19:50] Done (elapsed time=00:13:16, CPU time=00:13:16, peak memory=17.7gb)