[2026-06-03T20:54:41] Launching Arriba 2.4.0
[2026-06-03T20:54:41] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:54:49] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:54:52] Reading chimeric alignments from 'aih-tih-sc-da06ce-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=15703561)
[2026-06-03T21:02:21] Marking multi-mapping alignments (marked=11379992)
[2026-06-03T21:02:27] Detecting strandedness (reverse)
[2026-06-03T21:02:27] Assigning strands to alignments 
[2026-06-03T21:02:30] Annotating alignments 
[2026-06-03T21:03:23] Filtering duplicates (remaining=7133495)
[2026-06-03T21:03:33] 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=6243565)
[2026-06-03T21:03:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6243565)
[2026-06-03T21:03:39] Filtering viral contigs with expression lower than the top 5 (remaining=6243565)
[2026-06-03T21:03:46] Filtering viral contigs with less than 5% coverage (remaining=6243565)
[2026-06-03T21:03:49] Estimating fragment length (mate gap mean=-84.4913, mate gap stddev=31.0574, read length mean=125.367)
[2026-06-03T21:03:49] Filtering read-through fragments with a distance <=10000bp (remaining=6054402)
[2026-06-03T21:03:52] Filtering inconsistently clipped mates (remaining=5951968)
[2026-06-03T21:03:56] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5778307)
[2026-06-03T21:04:02] Filtering fragments with small insert size (remaining=5776761)
[2026-06-03T21:04:05] Filtering alignments with long gaps (remaining=5776760)
[2026-06-03T21:04:08] Filtering fragments with both mates in the same gene (remaining=5775717)
[2026-06-03T21:04:11] Filtering fusions arising from hairpin structures (remaining=5415606)
[2026-06-03T21:04:14] Filtering reads with a mismatch p-value <=0.01 (remaining=1761657)
[2026-06-03T21:04:30] Filtering reads with low entropy (k-mer content >=60%) (remaining=757433)
[2026-06-03T21:04:41] Finding fusions and counting supporting reads (total=600294)
[2026-06-03T21:05:03] Merging adjacent fusion breakpoints (remaining=590405)
[2026-06-03T21:05:05] Filtering multi-mapping fusions by alignment score and read support (remaining=363664)
[2026-06-03T21:05:55] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T21:06:03] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=360891)
[2026-06-03T21:06:04] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=216640)
[2026-06-03T21:06:05] Filtering fusions with <2 supporting reads (remaining=23902)
[2026-06-03T21:06:06] Filtering fusions with an e-value >=0.3 (remaining=7089)
[2026-06-03T21:06:07] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7134)
[2026-06-03T21:06:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6940)
[2026-06-03T21:06:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6940)
[2026-06-03T21:06:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5050)
[2026-06-03T21:06:21] Searching for fusions with spliced split reads (remaining=5136)
[2026-06-03T21:06:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=3013)
[2026-06-03T21:06:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2971)
[2026-06-03T21:06:30] Searching for fusions with >=4 spliced events (remaining=3278)
[2026-06-03T21:06:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1285)
[2026-06-03T21:06:46] Filtering fusions with anchors <=23nt (remaining=862)
[2026-06-03T21:06:47] Filtering end-to-end fusions with low support (remaining=766)
[2026-06-03T21:06:48] Filtering fusions with no coverage around the breakpoints (remaining=739)
[2026-06-03T21:06:49] Indexing gene sequences 
[2026-06-03T21:06:53] Filtering genes with >=30% identity (remaining=295)
[2026-06-03T21:06:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=167)
[2026-06-03T21:06:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=164)
[2026-06-03T21:06:59] Searching for additional isoforms (remaining=195)
[2026-06-03T21:07:00] Assigning confidence scores to events 
[2026-06-03T21:07:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T21:07:04] Writing fusions to file 'aih-tih-sc-da06ce-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T21:07:06] Writing discarded fusions to file 'aih-tih-sc-da06ce-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T21:07:36] Freeing resources
[2026-06-03T21:08:00] Done (elapsed time=00:13:19, CPU time=00:13:18, peak memory=20.9gb)