[2026-06-08T09:02:21] Launching Arriba 2.4.0
[2026-06-08T09:02:21] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:02:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:02:42] Reading chimeric alignments from 'aih-tih-sc-835699-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10228976)
[2026-06-08T09:10:51] Marking multi-mapping alignments (marked=6518815)
[2026-06-08T09:10:55] Detecting strandedness (reverse)
[2026-06-08T09:10:55] Assigning strands to alignments 
[2026-06-08T09:10:57] Annotating alignments 
[2026-06-08T09:11:29] Filtering duplicates (remaining=5741280)
[2026-06-08T09:11:35] 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=5478647)
[2026-06-08T09:11:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5478647)
[2026-06-08T09:11:39] Filtering viral contigs with expression lower than the top 5 (remaining=5478647)
[2026-06-08T09:11:43] Filtering viral contigs with less than 5% coverage (remaining=5478647)
[2026-06-08T09:11:45] Estimating fragment length (mate gap mean=-86.7832, mate gap stddev=29.1428, read length mean=131.24)
[2026-06-08T09:11:45] Filtering read-through fragments with a distance <=10000bp (remaining=5062252)
[2026-06-08T09:11:47] Filtering inconsistently clipped mates (remaining=4959034)
[2026-06-08T09:11:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4845138)
[2026-06-08T09:11:53] Filtering fragments with small insert size (remaining=4844382)
[2026-06-08T09:11:55] Filtering alignments with long gaps (remaining=4844381)
[2026-06-08T09:11:57] Filtering fragments with both mates in the same gene (remaining=4843386)
[2026-06-08T09:11:59] Filtering fusions arising from hairpin structures (remaining=4482559)
[2026-06-08T09:12:01] Filtering reads with a mismatch p-value <=0.01 (remaining=2071889)
[2026-06-08T09:12:14] Filtering reads with low entropy (k-mer content >=60%) (remaining=919181)
[2026-06-08T09:12:24] Finding fusions and counting supporting reads (total=673702)
[2026-06-08T09:12:39] Merging adjacent fusion breakpoints (remaining=663675)
[2026-06-08T09:12:41] Filtering multi-mapping fusions by alignment score and read support (remaining=430308)
[2026-06-08T09:13:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:13:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=427481)
[2026-06-08T09:13:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=211125)
[2026-06-08T09:13:17] Filtering fusions with <2 supporting reads (remaining=32684)
[2026-06-08T09:13:18] Filtering fusions with an e-value >=0.3 (remaining=10236)
[2026-06-08T09:13:19] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10302)
[2026-06-08T09:13:22] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10230)
[2026-06-08T09:13:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10230)
[2026-06-08T09:13:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7453)
[2026-06-08T09:13:28] Searching for fusions with spliced split reads (remaining=7571)
[2026-06-08T09:13:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=4700)
[2026-06-08T09:13:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4646)
[2026-06-08T09:13:34] Searching for fusions with >=4 spliced events (remaining=5283)
[2026-06-08T09:13:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1725)
[2026-06-08T09:13:51] Filtering fusions with anchors <=23nt (remaining=1281)
[2026-06-08T09:13:52] Filtering end-to-end fusions with low support (remaining=1233)
[2026-06-08T09:13:53] Filtering fusions with no coverage around the breakpoints (remaining=1207)
[2026-06-08T09:13:53] Indexing gene sequences 
[2026-06-08T09:13:58] Filtering genes with >=30% identity (remaining=412)
[2026-06-08T09:14:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=190)
[2026-06-08T09:14:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=190)
[2026-06-08T09:14:03] Searching for additional isoforms (remaining=219)
[2026-06-08T09:14:05] Assigning confidence scores to events 
[2026-06-08T09:14:07] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:14:07] Writing fusions to file 'aih-tih-sc-835699-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:14:09] Writing discarded fusions to file 'aih-tih-sc-835699-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:14:32] Freeing resources
[2026-06-08T09:14:48] Done (elapsed time=00:12:27, CPU time=00:12:26, peak memory=14.9gb)