[2026-06-08T08:14:47] Launching Arriba 2.4.0
[2026-06-08T08:14:47] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:15:03] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:15:08] Reading chimeric alignments from 'aih-tih-sc-89cc59-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=12390804)
[2026-06-08T08:21:29] Marking multi-mapping alignments (marked=8903985)
[2026-06-08T08:21:34] Detecting strandedness (reverse)
[2026-06-08T08:21:34] Assigning strands to alignments 
[2026-06-08T08:21:36] Annotating alignments 
[2026-06-08T08:22:22] Filtering duplicates (remaining=3550776)
[2026-06-08T08:22:29] 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=3074543)
[2026-06-08T08:22:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3074543)
[2026-06-08T08:22:34] Filtering viral contigs with expression lower than the top 5 (remaining=3074543)
[2026-06-08T08:22:40] Filtering viral contigs with less than 5% coverage (remaining=3074543)
[2026-06-08T08:22:43] Estimating fragment length (mate gap mean=-80.0935, mate gap stddev=28.715, read length mean=118.834)
[2026-06-08T08:22:43] Filtering read-through fragments with a distance <=10000bp (remaining=2944934)
[2026-06-08T08:22:45] Filtering inconsistently clipped mates (remaining=2874988)
[2026-06-08T08:22:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2772323)
[2026-06-08T08:22:52] Filtering fragments with small insert size (remaining=2771254)
[2026-06-08T08:22:54] Filtering alignments with long gaps (remaining=2771254)
[2026-06-08T08:22:57] Filtering fragments with both mates in the same gene (remaining=2770459)
[2026-06-08T08:22:59] Filtering fusions arising from hairpin structures (remaining=2638649)
[2026-06-08T08:23:02] Filtering reads with a mismatch p-value <=0.01 (remaining=950527)
[2026-06-08T08:23:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=284011)
[2026-06-08T08:23:17] Finding fusions and counting supporting reads (total=235957)
[2026-06-08T08:23:33] Merging adjacent fusion breakpoints (remaining=232807)
[2026-06-08T08:23:33] Filtering multi-mapping fusions by alignment score and read support (remaining=119564)
[2026-06-08T08:24:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:24:15] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=118514)
[2026-06-08T08:24:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=67190)
[2026-06-08T08:24:16] Filtering fusions with <2 supporting reads (remaining=5678)
[2026-06-08T08:24:16] Filtering fusions with an e-value >=0.3 (remaining=1228)
[2026-06-08T08:24:16] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1264)
[2026-06-08T08:24:20] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1192)
[2026-06-08T08:24:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1192)
[2026-06-08T08:24:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1179)
[2026-06-08T08:24:25] Searching for fusions with spliced split reads (remaining=1225)
[2026-06-08T08:24:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=934)
[2026-06-08T08:24:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=924)
[2026-06-08T08:24:31] Searching for fusions with >=4 spliced events (remaining=1000)
[2026-06-08T08:24:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=399)
[2026-06-08T08:24:49] Filtering fusions with anchors <=23nt (remaining=314)
[2026-06-08T08:24:50] Filtering end-to-end fusions with low support (remaining=303)
[2026-06-08T08:24:50] Filtering fusions with no coverage around the breakpoints (remaining=290)
[2026-06-08T08:24:51] Indexing gene sequences 
[2026-06-08T08:24:53] Filtering genes with >=30% identity (remaining=94)
[2026-06-08T08:24:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=29)
[2026-06-08T08:24:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=29)
[2026-06-08T08:24:55] Searching for additional isoforms (remaining=31)
[2026-06-08T08:24:56] Assigning confidence scores to events 
[2026-06-08T08:24:58] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:24:58] Writing fusions to file 'aih-tih-sc-89cc59-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:24:59] Writing discarded fusions to file 'aih-tih-sc-89cc59-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:25:19] Freeing resources
[2026-06-08T08:25:39] Done (elapsed time=00:10:52, CPU time=00:10:51, peak memory=16.5gb)