[2026-06-08T08:51:08] Launching Arriba 2.4.0
[2026-06-08T08:51:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:51:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:51:22] Reading chimeric alignments from 'aih-tih-sc-7d62c4-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=12488565)
[2026-06-08T08:58:49] Marking multi-mapping alignments (marked=7976124)
[2026-06-08T08:58:55] Detecting strandedness (reverse)
[2026-06-08T08:58:55] Assigning strands to alignments 
[2026-06-08T08:58:58] Annotating alignments 
[2026-06-08T08:59:42] Filtering duplicates (remaining=7355500)
[2026-06-08T08:59:52] 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=7079335)
[2026-06-08T08:59:54] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7079335)
[2026-06-08T08:59:57] Filtering viral contigs with expression lower than the top 5 (remaining=7079335)
[2026-06-08T09:00:03] Filtering viral contigs with less than 5% coverage (remaining=7079335)
[2026-06-08T09:00:06] Estimating fragment length (mate gap mean=-89.0881, mate gap stddev=28.4901, read length mean=136.391)
[2026-06-08T09:00:07] Filtering read-through fragments with a distance <=10000bp (remaining=6719356)
[2026-06-08T09:00:09] Filtering inconsistently clipped mates (remaining=6621370)
[2026-06-08T09:00:12] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6465097)
[2026-06-08T09:00:17] Filtering fragments with small insert size (remaining=6464391)
[2026-06-08T09:00:20] Filtering alignments with long gaps (remaining=6464390)
[2026-06-08T09:00:23] Filtering fragments with both mates in the same gene (remaining=6463394)
[2026-06-08T09:00:26] Filtering fusions arising from hairpin structures (remaining=6175744)
[2026-06-08T09:00:29] Filtering reads with a mismatch p-value <=0.01 (remaining=2924881)
[2026-06-08T09:00:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=986339)
[2026-06-08T09:00:58] Finding fusions and counting supporting reads (total=739095)
[2026-06-08T09:01:27] Merging adjacent fusion breakpoints (remaining=731730)
[2026-06-08T09:01:29] Filtering multi-mapping fusions by alignment score and read support (remaining=455305)
[2026-06-08T09:02:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:02:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=453194)
[2026-06-08T09:02:23] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=254585)
[2026-06-08T09:02:24] Filtering fusions with <2 supporting reads (remaining=33450)
[2026-06-08T09:02:26] Filtering fusions with an e-value >=0.3 (remaining=8866)
[2026-06-08T09:02:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8915)
[2026-06-08T09:02:32] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8805)
[2026-06-08T09:02:33] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8805)
[2026-06-08T09:02:35] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7788)
[2026-06-08T09:02:41] Searching for fusions with spliced split reads (remaining=7812)
[2026-06-08T09:02:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=4659)
[2026-06-08T09:02:50] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4600)
[2026-06-08T09:02:50] Searching for fusions with >=4 spliced events (remaining=5618)
[2026-06-08T09:02:53] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2193)
[2026-06-08T09:03:10] Filtering fusions with anchors <=23nt (remaining=1840)
[2026-06-08T09:03:11] Filtering end-to-end fusions with low support (remaining=1782)
[2026-06-08T09:03:12] Filtering fusions with no coverage around the breakpoints (remaining=1736)
[2026-06-08T09:03:13] Indexing gene sequences 
[2026-06-08T09:03:21] Filtering genes with >=30% identity (remaining=577)
[2026-06-08T09:03:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=296)
[2026-06-08T09:03:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=259)
[2026-06-08T09:03:35] Searching for additional isoforms (remaining=340)
[2026-06-08T09:03:37] Assigning confidence scores to events 
[2026-06-08T09:03:41] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:03:41] Writing fusions to file 'aih-tih-sc-7d62c4-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:03:45] Writing discarded fusions to file 'aih-tih-sc-7d62c4-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:04:22] Freeing resources
[2026-06-08T09:04:44] Done (elapsed time=00:13:36, CPU time=00:13:35, peak memory=16.8gb)