[2026-06-08T08:32:11] Launching Arriba 2.4.0
[2026-06-08T08:32:11] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:20] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:24] Reading chimeric alignments from 'aih-tih-sc-7c8bae-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11342393)
[2026-06-08T08:39:13] Marking multi-mapping alignments (marked=7123413)
[2026-06-08T08:39:17] Detecting strandedness (reverse)
[2026-06-08T08:39:17] Assigning strands to alignments 
[2026-06-08T08:39:19] Annotating alignments 
[2026-06-08T08:39:56] Filtering duplicates (remaining=7872913)
[2026-06-08T08:40:04] 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=7673992)
[2026-06-08T08:40:06] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7673992)
[2026-06-08T08:40:08] Filtering viral contigs with expression lower than the top 5 (remaining=7673992)
[2026-06-08T08:40:13] Filtering viral contigs with less than 5% coverage (remaining=7673992)
[2026-06-08T08:40:16] Estimating fragment length (mate gap mean=-84.4538, mate gap stddev=29.9361, read length mean=136.876)
[2026-06-08T08:40:16] Filtering read-through fragments with a distance <=10000bp (remaining=7345093)
[2026-06-08T08:40:18] Filtering inconsistently clipped mates (remaining=7274605)
[2026-06-08T08:40:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7151568)
[2026-06-08T08:40:25] Filtering fragments with small insert size (remaining=7151067)
[2026-06-08T08:40:27] Filtering alignments with long gaps (remaining=7151067)
[2026-06-08T08:40:29] Filtering fragments with both mates in the same gene (remaining=7149960)
[2026-06-08T08:40:32] Filtering fusions arising from hairpin structures (remaining=6894038)
[2026-06-08T08:40:34] Filtering reads with a mismatch p-value <=0.01 (remaining=3494445)
[2026-06-08T08:40:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=1147672)
[2026-06-08T08:41:03] Finding fusions and counting supporting reads (total=804571)
[2026-06-08T08:41:22] Merging adjacent fusion breakpoints (remaining=799074)
[2026-06-08T08:41:24] Filtering multi-mapping fusions by alignment score and read support (remaining=532107)
[2026-06-08T08:41:59] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:42:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=530218)
[2026-06-08T08:42:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=312526)
[2026-06-08T08:42:10] Filtering fusions with <2 supporting reads (remaining=40503)
[2026-06-08T08:42:11] Filtering fusions with an e-value >=0.3 (remaining=12307)
[2026-06-08T08:42:12] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12357)
[2026-06-08T08:42:16] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12302)
[2026-06-08T08:42:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12303)
[2026-06-08T08:42:19] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8291)
[2026-06-08T08:42:24] Searching for fusions with spliced split reads (remaining=8362)
[2026-06-08T08:42:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=4697)
[2026-06-08T08:42:32] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4644)
[2026-06-08T08:42:33] Searching for fusions with >=4 spliced events (remaining=5877)
[2026-06-08T08:42:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2416)
[2026-06-08T08:42:49] Filtering fusions with anchors <=23nt (remaining=2025)
[2026-06-08T08:42:50] Filtering end-to-end fusions with low support (remaining=1976)
[2026-06-08T08:42:51] Filtering fusions with no coverage around the breakpoints (remaining=1941)
[2026-06-08T08:42:52] Indexing gene sequences 
[2026-06-08T08:43:00] Filtering genes with >=30% identity (remaining=664)
[2026-06-08T08:43:05] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=358)
[2026-06-08T08:43:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=234)
[2026-06-08T08:43:16] Searching for additional isoforms (remaining=353)
[2026-06-08T08:43:17] Assigning confidence scores to events 
[2026-06-08T08:43:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:43:21] Writing fusions to file 'aih-tih-sc-7c8bae-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:43:24] Writing discarded fusions to file 'aih-tih-sc-7c8bae-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:43:56] Freeing resources
[2026-06-08T08:44:14] Done (elapsed time=00:12:03, CPU time=00:12:01, peak memory=15.5gb)