[2026-06-08T08:45:58] Launching Arriba 2.4.0
[2026-06-08T08:45:58] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:13] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:46:18] Reading chimeric alignments from 'aih-tih-sc-d5506e-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10044660)
[2026-06-08T08:53:57] Marking multi-mapping alignments (marked=6646253)
[2026-06-08T08:54:00] Detecting strandedness (reverse)
[2026-06-08T08:54:00] Assigning strands to alignments 
[2026-06-08T08:54:02] Annotating alignments 
[2026-06-08T08:54:35] Filtering duplicates (remaining=4274291)
[2026-06-08T08:54:40] 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=4032082)
[2026-06-08T08:54:42] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4032082)
[2026-06-08T08:54:43] Filtering viral contigs with expression lower than the top 5 (remaining=4032082)
[2026-06-08T08:54:47] Filtering viral contigs with less than 5% coverage (remaining=4032082)
[2026-06-08T08:54:49] Estimating fragment length (mate gap mean=-87.3755, mate gap stddev=27.951, read length mean=129.838)
[2026-06-08T08:54:49] Filtering read-through fragments with a distance <=10000bp (remaining=3898747)
[2026-06-08T08:54:51] Filtering inconsistently clipped mates (remaining=3844023)
[2026-06-08T08:54:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3731199)
[2026-06-08T08:54:56] Filtering fragments with small insert size (remaining=3730581)
[2026-06-08T08:54:58] Filtering alignments with long gaps (remaining=3730581)
[2026-06-08T08:55:00] Filtering fragments with both mates in the same gene (remaining=3729667)
[2026-06-08T08:55:01] Filtering fusions arising from hairpin structures (remaining=3610202)
[2026-06-08T08:55:03] Filtering reads with a mismatch p-value <=0.01 (remaining=1462475)
[2026-06-08T08:55:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=387755)
[2026-06-08T08:55:20] Finding fusions and counting supporting reads (total=290150)
[2026-06-08T08:55:35] Merging adjacent fusion breakpoints (remaining=287909)
[2026-06-08T08:55:36] Filtering multi-mapping fusions by alignment score and read support (remaining=172596)
[2026-06-08T08:56:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:56:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=171598)
[2026-06-08T08:56:14] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=105991)
[2026-06-08T08:56:15] Filtering fusions with <2 supporting reads (remaining=15337)
[2026-06-08T08:56:15] Filtering fusions with an e-value >=0.3 (remaining=5036)
[2026-06-08T08:56:16] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5071)
[2026-06-08T08:56:18] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5016)
[2026-06-08T08:56:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5016)
[2026-06-08T08:56:20] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3306)
[2026-06-08T08:56:24] Searching for fusions with spliced split reads (remaining=3351)
[2026-06-08T08:56:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=2465)
[2026-06-08T08:56:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2428)
[2026-06-08T08:56:30] Searching for fusions with >=4 spliced events (remaining=2645)
[2026-06-08T08:56:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=754)
[2026-06-08T08:56:49] Filtering fusions with anchors <=23nt (remaining=598)
[2026-06-08T08:56:50] Filtering end-to-end fusions with low support (remaining=585)
[2026-06-08T08:56:50] Filtering fusions with no coverage around the breakpoints (remaining=563)
[2026-06-08T08:56:51] Indexing gene sequences 
[2026-06-08T08:56:54] Filtering genes with >=30% identity (remaining=195)
[2026-06-08T08:56:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=123)
[2026-06-08T08:56:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=123)
[2026-06-08T08:56:59] Searching for additional isoforms (remaining=137)
[2026-06-08T08:56:59] Assigning confidence scores to events 
[2026-06-08T08:57:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:57:02] Writing fusions to file 'aih-tih-sc-d5506e-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:57:03] Writing discarded fusions to file 'aih-tih-sc-d5506e-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:57:24] Freeing resources
[2026-06-08T08:57:40] Done (elapsed time=00:11:42, CPU time=00:11:41, peak memory=14.1gb)