[2026-06-08T09:04:22] Launching Arriba 2.4.0
[2026-06-08T09:04:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:04:31] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:04:35] Reading chimeric alignments from 'aih-tih-sc-951f98-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10666260)
[2026-06-08T09:11:36] Marking multi-mapping alignments (marked=6779048)
[2026-06-08T09:11:41] Detecting strandedness (reverse)
[2026-06-08T09:11:41] Assigning strands to alignments 
[2026-06-08T09:11:43] Annotating alignments 
[2026-06-08T09:12:20] Filtering duplicates (remaining=5576993)
[2026-06-08T09:12:26] 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=5304984)
[2026-06-08T09:12:28] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5304984)
[2026-06-08T09:12:30] Filtering viral contigs with expression lower than the top 5 (remaining=5304984)
[2026-06-08T09:12:35] Filtering viral contigs with less than 5% coverage (remaining=5304984)
[2026-06-08T09:12:38] Estimating fragment length (mate gap mean=-88.8596, mate gap stddev=29.1834, read length mean=133.014)
[2026-06-08T09:12:38] Filtering read-through fragments with a distance <=10000bp (remaining=5016058)
[2026-06-08T09:12:40] Filtering inconsistently clipped mates (remaining=4928516)
[2026-06-08T09:12:42] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4776788)
[2026-06-08T09:12:46] Filtering fragments with small insert size (remaining=4776202)
[2026-06-08T09:12:48] Filtering alignments with long gaps (remaining=4776202)
[2026-06-08T09:12:50] Filtering fragments with both mates in the same gene (remaining=4775319)
[2026-06-08T09:12:52] Filtering fusions arising from hairpin structures (remaining=4511717)
[2026-06-08T09:12:54] Filtering reads with a mismatch p-value <=0.01 (remaining=2002673)
[2026-06-08T09:13:07] Filtering reads with low entropy (k-mer content >=60%) (remaining=795836)
[2026-06-08T09:13:17] Finding fusions and counting supporting reads (total=631561)
[2026-06-08T09:13:34] Merging adjacent fusion breakpoints (remaining=624641)
[2026-06-08T09:13:35] Filtering multi-mapping fusions by alignment score and read support (remaining=373181)
[2026-06-08T09:14:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:14:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=370949)
[2026-06-08T09:14:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=209969)
[2026-06-08T09:14:19] Filtering fusions with <2 supporting reads (remaining=29796)
[2026-06-08T09:14:19] Filtering fusions with an e-value >=0.3 (remaining=9646)
[2026-06-08T09:14:20] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9695)
[2026-06-08T09:14:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9562)
[2026-06-08T09:14:24] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9568)
[2026-06-08T09:14:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6733)
[2026-06-08T09:14:31] Searching for fusions with spliced split reads (remaining=6855)
[2026-06-08T09:14:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=4570)
[2026-06-08T09:14:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4498)
[2026-06-08T09:14:37] Searching for fusions with >=4 spliced events (remaining=5102)
[2026-06-08T09:14:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1972)
[2026-06-08T09:15:01] Filtering fusions with anchors <=23nt (remaining=1331)
[2026-06-08T09:15:01] Filtering end-to-end fusions with low support (remaining=1270)
[2026-06-08T09:15:02] Filtering fusions with no coverage around the breakpoints (remaining=1216)
[2026-06-08T09:15:03] Indexing gene sequences 
[2026-06-08T09:15:08] Filtering genes with >=30% identity (remaining=432)
[2026-06-08T09:15:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=225)
[2026-06-08T09:15:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=197)
[2026-06-08T09:15:15] Searching for additional isoforms (remaining=232)
[2026-06-08T09:15:17] Assigning confidence scores to events 
[2026-06-08T09:15:20] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:15:20] Writing fusions to file 'aih-tih-sc-951f98-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:15:22] Writing discarded fusions to file 'aih-tih-sc-951f98-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:15:51] Freeing resources
[2026-06-08T09:16:10] Done (elapsed time=00:11:48, CPU time=00:11:47, peak memory=15.3gb)