[2026-06-08T08:53:08] Launching Arriba 2.4.0
[2026-06-08T08:53:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:53:26] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:53:33] Reading chimeric alignments from 'aih-tih-sc-099ac4-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11862241)
[2026-06-08T09:03:58] Marking multi-mapping alignments (marked=7655515)
[2026-06-08T09:04:04] Detecting strandedness (reverse)
[2026-06-08T09:04:04] Assigning strands to alignments 
[2026-06-08T09:04:06] Annotating alignments 
[2026-06-08T09:04:45] Filtering duplicates (remaining=7448385)
[2026-06-08T09:04:54] 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=7118460)
[2026-06-08T09:04:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7118460)
[2026-06-08T09:04:59] Filtering viral contigs with expression lower than the top 5 (remaining=7118460)
[2026-06-08T09:05:04] Filtering viral contigs with less than 5% coverage (remaining=7118460)
[2026-06-08T09:05:07] Estimating fragment length (mate gap mean=-87.257, mate gap stddev=28.7926, read length mean=133.113)
[2026-06-08T09:05:07] Filtering read-through fragments with a distance <=10000bp (remaining=6782068)
[2026-06-08T09:05:10] Filtering inconsistently clipped mates (remaining=6664340)
[2026-06-08T09:05:12] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6503859)
[2026-06-08T09:05:17] Filtering fragments with small insert size (remaining=6503298)
[2026-06-08T09:05:20] Filtering alignments with long gaps (remaining=6503298)
[2026-06-08T09:05:23] Filtering fragments with both mates in the same gene (remaining=6502369)
[2026-06-08T09:05:26] Filtering fusions arising from hairpin structures (remaining=6138288)
[2026-06-08T09:05:29] Filtering reads with a mismatch p-value <=0.01 (remaining=3010267)
[2026-06-08T09:05:50] Filtering reads with low entropy (k-mer content >=60%) (remaining=1069139)
[2026-06-08T09:06:06] Finding fusions and counting supporting reads (total=723073)
[2026-06-08T09:06:27] Merging adjacent fusion breakpoints (remaining=716204)
[2026-06-08T09:06:28] Filtering multi-mapping fusions by alignment score and read support (remaining=439572)
[2026-06-08T09:07:05] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:07:12] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=437680)
[2026-06-08T09:07:13] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=273186)
[2026-06-08T09:07:14] Filtering fusions with <2 supporting reads (remaining=36119)
[2026-06-08T09:07:15] Filtering fusions with an e-value >=0.3 (remaining=8699)
[2026-06-08T09:07:16] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8763)
[2026-06-08T09:07:20] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8654)
[2026-06-08T09:07:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8654)
[2026-06-08T09:07:22] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7745)
[2026-06-08T09:07:28] Searching for fusions with spliced split reads (remaining=7773)
[2026-06-08T09:07:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=4933)
[2026-06-08T09:07:35] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4895)
[2026-06-08T09:07:36] Searching for fusions with >=4 spliced events (remaining=5778)
[2026-06-08T09:07:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2117)
[2026-06-08T09:07:59] Filtering fusions with anchors <=23nt (remaining=1733)
[2026-06-08T09:07:59] Filtering end-to-end fusions with low support (remaining=1682)
[2026-06-08T09:08:00] Filtering fusions with no coverage around the breakpoints (remaining=1643)
[2026-06-08T09:08:01] Indexing gene sequences 
[2026-06-08T09:08:08] Filtering genes with >=30% identity (remaining=499)
[2026-06-08T09:08:11] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=256)
[2026-06-08T09:08:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=214)
[2026-06-08T09:08:20] Searching for additional isoforms (remaining=307)
[2026-06-08T09:08:22] Assigning confidence scores to events 
[2026-06-08T09:08:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:08:26] Writing fusions to file 'aih-tih-sc-099ac4-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:08:29] Writing discarded fusions to file 'aih-tih-sc-099ac4-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:09:04] Freeing resources
[2026-06-08T09:09:23] Done (elapsed time=00:16:15, CPU time=00:16:14, peak memory=16.3gb)