[2026-06-08T08:46:18] Launching Arriba 2.4.0
[2026-06-08T08:46:18] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:32] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:46:36] Reading chimeric alignments from 'aih-tih-sc-1dd7a6-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10490928)
[2026-06-08T08:54:37] Marking multi-mapping alignments (marked=6739443)
[2026-06-08T08:54:42] Detecting strandedness (reverse)
[2026-06-08T08:54:42] Assigning strands to alignments 
[2026-06-08T08:54:44] Annotating alignments 
[2026-06-08T08:55:18] Filtering duplicates (remaining=4667150)
[2026-06-08T08:55:24] 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=4414916)
[2026-06-08T08:55:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4414916)
[2026-06-08T08:55:28] Filtering viral contigs with expression lower than the top 5 (remaining=4414916)
[2026-06-08T08:55:33] Filtering viral contigs with less than 5% coverage (remaining=4414916)
[2026-06-08T08:55:35] Estimating fragment length (mate gap mean=-84.0833, mate gap stddev=28.4398, read length mean=125.964)
[2026-06-08T08:55:35] Filtering read-through fragments with a distance <=10000bp (remaining=4150694)
[2026-06-08T08:55:37] Filtering inconsistently clipped mates (remaining=4072630)
[2026-06-08T08:55:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3950376)
[2026-06-08T08:55:43] Filtering fragments with small insert size (remaining=3949407)
[2026-06-08T08:55:46] Filtering alignments with long gaps (remaining=3949407)
[2026-06-08T08:55:48] Filtering fragments with both mates in the same gene (remaining=3948493)
[2026-06-08T08:55:50] Filtering fusions arising from hairpin structures (remaining=3746004)
[2026-06-08T08:55:52] Filtering reads with a mismatch p-value <=0.01 (remaining=1634301)
[2026-06-08T08:56:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=609942)
[2026-06-08T08:56:13] Finding fusions and counting supporting reads (total=518187)
[2026-06-08T08:56:29] Merging adjacent fusion breakpoints (remaining=513096)
[2026-06-08T08:56:30] Filtering multi-mapping fusions by alignment score and read support (remaining=309876)
[2026-06-08T08:57:03] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=307526)
[2026-06-08T08:57:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=160536)
[2026-06-08T08:57:10] Filtering fusions with <2 supporting reads (remaining=18411)
[2026-06-08T08:57:10] Filtering fusions with an e-value >=0.3 (remaining=4977)
[2026-06-08T08:57:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5013)
[2026-06-08T08:57:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4958)
[2026-06-08T08:57:14] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4958)
[2026-06-08T08:57:15] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3995)
[2026-06-08T08:57:20] Searching for fusions with spliced split reads (remaining=4072)
[2026-06-08T08:57:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=2828)
[2026-06-08T08:57:25] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2801)
[2026-06-08T08:57:26] Searching for fusions with >=4 spliced events (remaining=3130)
[2026-06-08T08:57:27] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1149)
[2026-06-08T08:57:44] Filtering fusions with anchors <=23nt (remaining=906)
[2026-06-08T08:57:44] Filtering end-to-end fusions with low support (remaining=883)
[2026-06-08T08:57:45] Filtering fusions with no coverage around the breakpoints (remaining=861)
[2026-06-08T08:57:45] Indexing gene sequences 
[2026-06-08T08:57:50] Filtering genes with >=30% identity (remaining=294)
[2026-06-08T08:57:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=114)
[2026-06-08T08:57:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=111)
[2026-06-08T08:57:54] Searching for additional isoforms (remaining=137)
[2026-06-08T08:57:55] Assigning confidence scores to events 
[2026-06-08T08:57:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:57:57] Writing fusions to file 'aih-tih-sc-1dd7a6-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:57:59] Writing discarded fusions to file 'aih-tih-sc-1dd7a6-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:58:24] Freeing resources
[2026-06-08T08:58:41] Done (elapsed time=00:12:23, CPU time=00:12:23, peak memory=14.9gb)