[2026-06-08T08:50:02] Launching Arriba 2.4.0
[2026-06-08T08:50:02] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:50:13] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:50:18] Reading chimeric alignments from 'aih-tih-sc-b157e9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=12956285)
[2026-06-08T08:57:18] Marking multi-mapping alignments (marked=8485104)
[2026-06-08T08:57:23] Detecting strandedness (reverse)
[2026-06-08T08:57:23] Assigning strands to alignments 
[2026-06-08T08:57:25] Annotating alignments 
[2026-06-08T08:58:05] Filtering duplicates (remaining=6549574)
[2026-06-08T08:58:14] 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=6250803)
[2026-06-08T08:58:16] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6250803)
[2026-06-08T08:58:19] Filtering viral contigs with expression lower than the top 5 (remaining=6250803)
[2026-06-08T08:58:25] Filtering viral contigs with less than 5% coverage (remaining=6250803)
[2026-06-08T08:58:27] Estimating fragment length (mate gap mean=-87.8152, mate gap stddev=27.9715, read length mean=129.01)
[2026-06-08T08:58:27] Filtering read-through fragments with a distance <=10000bp (remaining=5881795)
[2026-06-08T08:58:30] Filtering inconsistently clipped mates (remaining=5774757)
[2026-06-08T08:58:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5660125)
[2026-06-08T08:58:38] Filtering fragments with small insert size (remaining=5659544)
[2026-06-08T08:58:40] Filtering alignments with long gaps (remaining=5659544)
[2026-06-08T08:58:43] Filtering fragments with both mates in the same gene (remaining=5658657)
[2026-06-08T08:58:45] Filtering fusions arising from hairpin structures (remaining=5378089)
[2026-06-08T08:58:48] Filtering reads with a mismatch p-value <=0.01 (remaining=2408594)
[2026-06-08T08:59:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=784316)
[2026-06-08T08:59:14] Finding fusions and counting supporting reads (total=589212)
[2026-06-08T08:59:33] Merging adjacent fusion breakpoints (remaining=581433)
[2026-06-08T08:59:35] Filtering multi-mapping fusions by alignment score and read support (remaining=367429)
[2026-06-08T09:00:15] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=366098)
[2026-06-08T09:00:23] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=209937)
[2026-06-08T09:00:24] Filtering fusions with <2 supporting reads (remaining=28532)
[2026-06-08T09:00:24] Filtering fusions with an e-value >=0.3 (remaining=8694)
[2026-06-08T09:00:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8771)
[2026-06-08T09:00:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8698)
[2026-06-08T09:00:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8698)
[2026-06-08T09:00:32] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6161)
[2026-06-08T09:00:37] Searching for fusions with spliced split reads (remaining=6263)
[2026-06-08T09:00:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=4114)
[2026-06-08T09:00:44] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4062)
[2026-06-08T09:00:45] Searching for fusions with >=4 spliced events (remaining=4671)
[2026-06-08T09:00:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1771)
[2026-06-08T09:01:04] Filtering fusions with anchors <=23nt (remaining=1344)
[2026-06-08T09:01:05] Filtering end-to-end fusions with low support (remaining=1312)
[2026-06-08T09:01:06] Filtering fusions with no coverage around the breakpoints (remaining=1277)
[2026-06-08T09:01:06] Indexing gene sequences 
[2026-06-08T09:01:12] Filtering genes with >=30% identity (remaining=519)
[2026-06-08T09:01:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=282)
[2026-06-08T09:01:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=224)
[2026-06-08T09:01:23] Searching for additional isoforms (remaining=316)
[2026-06-08T09:01:24] Assigning confidence scores to events 
[2026-06-08T09:01:27] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:28] Writing fusions to file 'aih-tih-sc-b157e9-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:01:30] Writing discarded fusions to file 'aih-tih-sc-b157e9-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:58] Freeing resources
[2026-06-08T09:02:18] Done (elapsed time=00:12:16, CPU time=00:12:15, peak memory=17.2gb)