[2026-06-08T08:49:09] Launching Arriba 2.4.0
[2026-06-08T08:49:09] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:17] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:21] Reading chimeric alignments from 'aih-tih-sc-76a805-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=12811024)
[2026-06-08T08:56:29] Marking multi-mapping alignments (marked=8538010)
[2026-06-08T08:56:34] Detecting strandedness (reverse)
[2026-06-08T08:56:34] Assigning strands to alignments 
[2026-06-08T08:56:38] Annotating alignments 
[2026-06-08T08:57:21] Filtering duplicates (remaining=7480424)
[2026-06-08T08:57:31] 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=7108467)
[2026-06-08T08:57:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7108467)
[2026-06-08T08:57:37] Filtering viral contigs with expression lower than the top 5 (remaining=7108467)
[2026-06-08T08:57:44] Filtering viral contigs with less than 5% coverage (remaining=7108467)
[2026-06-08T08:57:47] Estimating fragment length (mate gap mean=-86.776, mate gap stddev=28.8603, read length mean=134.471)
[2026-06-08T08:57:47] Filtering read-through fragments with a distance <=10000bp (remaining=6706400)
[2026-06-08T08:57:50] Filtering inconsistently clipped mates (remaining=6610773)
[2026-06-08T08:57:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6464282)
[2026-06-08T08:57:59] Filtering fragments with small insert size (remaining=6463687)
[2026-06-08T08:58:02] Filtering alignments with long gaps (remaining=6463686)
[2026-06-08T08:58:05] Filtering fragments with both mates in the same gene (remaining=6462701)
[2026-06-08T08:58:08] Filtering fusions arising from hairpin structures (remaining=6143481)
[2026-06-08T08:58:12] Filtering reads with a mismatch p-value <=0.01 (remaining=3029336)
[2026-06-08T08:58:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=996115)
[2026-06-08T08:58:40] Finding fusions and counting supporting reads (total=712781)
[2026-06-08T08:59:02] Merging adjacent fusion breakpoints (remaining=705073)
[2026-06-08T08:59:04] Filtering multi-mapping fusions by alignment score and read support (remaining=426124)
[2026-06-08T08:59:49] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=423125)
[2026-06-08T08:59:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=236870)
[2026-06-08T09:00:00] Filtering fusions with <2 supporting reads (remaining=29746)
[2026-06-08T09:00:01] Filtering fusions with an e-value >=0.3 (remaining=9774)
[2026-06-08T09:00:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9847)
[2026-06-08T09:00:07] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9764)
[2026-06-08T09:00:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9764)
[2026-06-08T09:00:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6873)
[2026-06-08T09:00:17] Searching for fusions with spliced split reads (remaining=6981)
[2026-06-08T09:00:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=4078)
[2026-06-08T09:00:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4033)
[2026-06-08T09:00:26] Searching for fusions with >=4 spliced events (remaining=4738)
[2026-06-08T09:00:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1856)
[2026-06-08T09:00:46] Filtering fusions with anchors <=23nt (remaining=1505)
[2026-06-08T09:00:47] Filtering end-to-end fusions with low support (remaining=1457)
[2026-06-08T09:00:48] Filtering fusions with no coverage around the breakpoints (remaining=1412)
[2026-06-08T09:00:49] Indexing gene sequences 
[2026-06-08T09:00:55] Filtering genes with >=30% identity (remaining=471)
[2026-06-08T09:00:59] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=210)
[2026-06-08T09:01:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=183)
[2026-06-08T09:01:03] Searching for additional isoforms (remaining=228)
[2026-06-08T09:01:05] Assigning confidence scores to events 
[2026-06-08T09:01:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:10] Writing fusions to file 'aih-tih-sc-76a805-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:01:11] Writing discarded fusions to file 'aih-tih-sc-76a805-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:48] Freeing resources
[2026-06-08T09:02:09] Done (elapsed time=00:13:00, CPU time=00:12:58, peak memory=17.2gb)