[2026-06-08T08:48:25] Launching Arriba 2.4.0
[2026-06-08T08:48:25] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:34] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:39] Reading chimeric alignments from 'aih-tih-sc-6734d6-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=11318252)
[2026-06-08T08:55:40] Marking multi-mapping alignments (marked=7388063)
[2026-06-08T08:55:46] Detecting strandedness (reverse)
[2026-06-08T08:55:46] Assigning strands to alignments 
[2026-06-08T08:55:49] Annotating alignments 
[2026-06-08T08:56:27] Filtering duplicates (remaining=5971184)
[2026-06-08T08:56:35] 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=5557327)
[2026-06-08T08:56:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5557327)
[2026-06-08T08:56:40] Filtering viral contigs with expression lower than the top 5 (remaining=5557327)
[2026-06-08T08:56:45] Filtering viral contigs with less than 5% coverage (remaining=5557327)
[2026-06-08T08:56:48] Estimating fragment length (mate gap mean=-86.8691, mate gap stddev=29.4384, read length mean=132.168)
[2026-06-08T08:56:48] Filtering read-through fragments with a distance <=10000bp (remaining=5193740)
[2026-06-08T08:56:50] Filtering inconsistently clipped mates (remaining=5103023)
[2026-06-08T08:56:52] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4985609)
[2026-06-08T08:56:57] Filtering fragments with small insert size (remaining=4984713)
[2026-06-08T08:56:59] Filtering alignments with long gaps (remaining=4984713)
[2026-06-08T08:57:02] Filtering fragments with both mates in the same gene (remaining=4983866)
[2026-06-08T08:57:04] Filtering fusions arising from hairpin structures (remaining=4699332)
[2026-06-08T08:57:07] Filtering reads with a mismatch p-value <=0.01 (remaining=2144170)
[2026-06-08T08:57:21] Filtering reads with low entropy (k-mer content >=60%) (remaining=836488)
[2026-06-08T08:57:31] Finding fusions and counting supporting reads (total=660853)
[2026-06-08T08:57:49] Merging adjacent fusion breakpoints (remaining=654883)
[2026-06-08T08:57:51] Filtering multi-mapping fusions by alignment score and read support (remaining=415331)
[2026-06-08T08:58:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:35] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=412073)
[2026-06-08T08:58:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=213362)
[2026-06-08T08:58:37] Filtering fusions with <2 supporting reads (remaining=30070)
[2026-06-08T08:58:38] Filtering fusions with an e-value >=0.3 (remaining=10136)
[2026-06-08T08:58:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10195)
[2026-06-08T08:58:43] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10078)
[2026-06-08T08:58:44] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10078)
[2026-06-08T08:58:45] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6790)
[2026-06-08T08:58:50] Searching for fusions with spliced split reads (remaining=6882)
[2026-06-08T08:58:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=4227)
[2026-06-08T08:58:57] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4182)
[2026-06-08T08:58:57] Searching for fusions with >=4 spliced events (remaining=4839)
[2026-06-08T08:58:59] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1718)
[2026-06-08T08:59:14] Filtering fusions with anchors <=23nt (remaining=1292)
[2026-06-08T08:59:15] Filtering end-to-end fusions with low support (remaining=1239)
[2026-06-08T08:59:16] Filtering fusions with no coverage around the breakpoints (remaining=1219)
[2026-06-08T08:59:16] Indexing gene sequences 
[2026-06-08T08:59:21] Filtering genes with >=30% identity (remaining=416)
[2026-06-08T08:59:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=217)
[2026-06-08T08:59:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=200)
[2026-06-08T08:59:28] Searching for additional isoforms (remaining=239)
[2026-06-08T08:59:29] Assigning confidence scores to events 
[2026-06-08T08:59:32] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:32] Writing fusions to file 'aih-tih-sc-6734d6-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:34] Writing discarded fusions to file 'aih-tih-sc-6734d6-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:03] Freeing resources
[2026-06-08T09:00:20] Done (elapsed time=00:11:55, CPU time=00:11:54, peak memory=16gb)