[2026-06-08T08:59:19] Launching Arriba 2.4.0
[2026-06-08T08:59:19] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:59:34] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:59:38] Reading chimeric alignments from 'aih-tih-sc-b107e7-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10672414)
[2026-06-08T09:08:42] Marking multi-mapping alignments (marked=6789259)
[2026-06-08T09:08:47] Detecting strandedness (reverse)
[2026-06-08T09:08:47] Assigning strands to alignments 
[2026-06-08T09:08:49] Annotating alignments 
[2026-06-08T09:09:28] Filtering duplicates (remaining=5422807)
[2026-06-08T09:09:36] 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=5036434)
[2026-06-08T09:09:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5036434)
[2026-06-08T09:09:40] Filtering viral contigs with expression lower than the top 5 (remaining=5036434)
[2026-06-08T09:09:46] Filtering viral contigs with less than 5% coverage (remaining=5036434)
[2026-06-08T09:09:48] Estimating fragment length (mate gap mean=-86.6507, mate gap stddev=30.2646, read length mean=132.609)
[2026-06-08T09:09:49] Filtering read-through fragments with a distance <=10000bp (remaining=4786761)
[2026-06-08T09:09:51] Filtering inconsistently clipped mates (remaining=4711211)
[2026-06-08T09:09:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4594186)
[2026-06-08T09:09:58] Filtering fragments with small insert size (remaining=4593230)
[2026-06-08T09:10:01] Filtering alignments with long gaps (remaining=4593230)
[2026-06-08T09:10:03] Filtering fragments with both mates in the same gene (remaining=4592329)
[2026-06-08T09:10:06] Filtering fusions arising from hairpin structures (remaining=4337397)
[2026-06-08T09:10:09] Filtering reads with a mismatch p-value <=0.01 (remaining=1788663)
[2026-06-08T09:10:22] Filtering reads with low entropy (k-mer content >=60%) (remaining=708599)
[2026-06-08T09:10:32] Finding fusions and counting supporting reads (total=541938)
[2026-06-08T09:10:50] Merging adjacent fusion breakpoints (remaining=536666)
[2026-06-08T09:10:51] Filtering multi-mapping fusions by alignment score and read support (remaining=349517)
[2026-06-08T09:11:26] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:11:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=347161)
[2026-06-08T09:11:32] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=188308)
[2026-06-08T09:11:33] Filtering fusions with <2 supporting reads (remaining=24719)
[2026-06-08T09:11:34] Filtering fusions with an e-value >=0.3 (remaining=6978)
[2026-06-08T09:11:34] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7016)
[2026-06-08T09:11:38] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6960)
[2026-06-08T09:11:39] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6960)
[2026-06-08T09:11:40] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5081)
[2026-06-08T09:11:45] Searching for fusions with spliced split reads (remaining=5183)
[2026-06-08T09:11:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=3399)
[2026-06-08T09:11:50] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3344)
[2026-06-08T09:11:51] Searching for fusions with >=4 spliced events (remaining=3812)
[2026-06-08T09:11:52] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1333)
[2026-06-08T09:12:08] Filtering fusions with anchors <=23nt (remaining=1000)
[2026-06-08T09:12:09] Filtering end-to-end fusions with low support (remaining=941)
[2026-06-08T09:12:09] Filtering fusions with no coverage around the breakpoints (remaining=915)
[2026-06-08T09:12:10] Indexing gene sequences 
[2026-06-08T09:12:15] Filtering genes with >=30% identity (remaining=312)
[2026-06-08T09:12:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=166)
[2026-06-08T09:12:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=157)
[2026-06-08T09:12:20] Searching for additional isoforms (remaining=189)
[2026-06-08T09:12:21] Assigning confidence scores to events 
[2026-06-08T09:12:24] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:12:24] Writing fusions to file 'aih-tih-sc-b107e7-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:12:25] Writing discarded fusions to file 'aih-tih-sc-b107e7-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:12:53] Freeing resources
[2026-06-08T09:13:11] Done (elapsed time=00:13:52, CPU time=00:13:51, peak memory=15.3gb)