[2026-06-08T08:51:51] Launching Arriba 2.4.0
[2026-06-08T08:51:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:01] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:05] Reading chimeric alignments from 'aih-tih-sc-9fb608-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=11536761)
[2026-06-08T08:59:23] Marking multi-mapping alignments (marked=7687419)
[2026-06-08T08:59:28] Detecting strandedness (reverse)
[2026-06-08T08:59:28] Assigning strands to alignments 
[2026-06-08T08:59:31] Annotating alignments 
[2026-06-08T09:00:16] Filtering duplicates (remaining=5434882)
[2026-06-08T09:00:25] 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=5032172)
[2026-06-08T09:00:28] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5032172)
[2026-06-08T09:00:30] Filtering viral contigs with expression lower than the top 5 (remaining=5032172)
[2026-06-08T09:00:36] Filtering viral contigs with less than 5% coverage (remaining=5032172)
[2026-06-08T09:00:38] Estimating fragment length (mate gap mean=-86.5411, mate gap stddev=30.9557, read length mean=132.188)
[2026-06-08T09:00:39] Filtering read-through fragments with a distance <=10000bp (remaining=4808031)
[2026-06-08T09:00:41] Filtering inconsistently clipped mates (remaining=4725475)
[2026-06-08T09:00:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4595215)
[2026-06-08T09:00:49] Filtering fragments with small insert size (remaining=4594514)
[2026-06-08T09:00:53] Filtering alignments with long gaps (remaining=4594514)
[2026-06-08T09:00:57] Filtering fragments with both mates in the same gene (remaining=4593639)
[2026-06-08T09:01:00] Filtering fusions arising from hairpin structures (remaining=4297347)
[2026-06-08T09:01:03] Filtering reads with a mismatch p-value <=0.01 (remaining=1830521)
[2026-06-08T09:01:17] Filtering reads with low entropy (k-mer content >=60%) (remaining=656310)
[2026-06-08T09:01:27] Finding fusions and counting supporting reads (total=520847)
[2026-06-08T09:01:46] Merging adjacent fusion breakpoints (remaining=513948)
[2026-06-08T09:01:48] Filtering multi-mapping fusions by alignment score and read support (remaining=326625)
[2026-06-08T09:02:40] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:02:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=323521)
[2026-06-08T09:02:47] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=179052)
[2026-06-08T09:02:48] Filtering fusions with <2 supporting reads (remaining=25067)
[2026-06-08T09:02:49] Filtering fusions with an e-value >=0.3 (remaining=9179)
[2026-06-08T09:02:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9218)
[2026-06-08T09:02:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9061)
[2026-06-08T09:02:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9063)
[2026-06-08T09:02:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5857)
[2026-06-08T09:03:02] Searching for fusions with spliced split reads (remaining=5956)
[2026-06-08T09:03:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=3911)
[2026-06-08T09:03:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3843)
[2026-06-08T09:03:09] Searching for fusions with >=4 spliced events (remaining=4213)
[2026-06-08T09:03:11] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1365)
[2026-06-08T09:03:29] Filtering fusions with anchors <=23nt (remaining=900)
[2026-06-08T09:03:29] Filtering end-to-end fusions with low support (remaining=859)
[2026-06-08T09:03:30] Filtering fusions with no coverage around the breakpoints (remaining=826)
[2026-06-08T09:03:31] Indexing gene sequences 
[2026-06-08T09:03:37] Filtering genes with >=30% identity (remaining=335)
[2026-06-08T09:03:39] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=215)
[2026-06-08T09:03:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=202)
[2026-06-08T09:03:45] Searching for additional isoforms (remaining=239)
[2026-06-08T09:03:46] Assigning confidence scores to events 
[2026-06-08T09:03:50] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:03:50] Writing fusions to file 'aih-tih-sc-9fb608-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:03:52] Writing discarded fusions to file 'aih-tih-sc-9fb608-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:04:25] Freeing resources
[2026-06-08T09:04:46] Done (elapsed time=00:12:55, CPU time=00:12:53, peak memory=16.2gb)