[2026-06-08T08:45:56] Launching Arriba 2.4.0
[2026-06-08T08:45:56] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:06] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:46:10] Reading chimeric alignments from 'aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10557769)
[2026-06-08T08:53:00] Marking multi-mapping alignments (marked=6896205)
[2026-06-08T08:53:05] Detecting strandedness (reverse)
[2026-06-08T08:53:05] Assigning strands to alignments 
[2026-06-08T08:53:07] Annotating alignments 
[2026-06-08T08:53:43] Filtering duplicates (remaining=5861822)
[2026-06-08T08:53:50] 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=5593642)
[2026-06-08T08:53:52] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5593642)
[2026-06-08T08:53:54] Filtering viral contigs with expression lower than the top 5 (remaining=5593642)
[2026-06-08T08:53:59] Filtering viral contigs with less than 5% coverage (remaining=5593642)
[2026-06-08T08:54:01] Estimating fragment length (mate gap mean=-86.4257, mate gap stddev=28.2659, read length mean=127.836)
[2026-06-08T08:54:01] Filtering read-through fragments with a distance <=10000bp (remaining=5212473)
[2026-06-08T08:54:03] Filtering inconsistently clipped mates (remaining=5113781)
[2026-06-08T08:54:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4993168)
[2026-06-08T08:54:09] Filtering fragments with small insert size (remaining=4992451)
[2026-06-08T08:54:11] Filtering alignments with long gaps (remaining=4992451)
[2026-06-08T08:54:14] Filtering fragments with both mates in the same gene (remaining=4991572)
[2026-06-08T08:54:16] Filtering fusions arising from hairpin structures (remaining=4653175)
[2026-06-08T08:54:18] Filtering reads with a mismatch p-value <=0.01 (remaining=2075393)
[2026-06-08T08:54:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=926477)
[2026-06-08T08:54:42] Finding fusions and counting supporting reads (total=709250)
[2026-06-08T08:54:59] Merging adjacent fusion breakpoints (remaining=698142)
[2026-06-08T08:55:01] Filtering multi-mapping fusions by alignment score and read support (remaining=428663)
[2026-06-08T08:55:36] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:55:43] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=426533)
[2026-06-08T08:55:44] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=233482)
[2026-06-08T08:55:45] Filtering fusions with <2 supporting reads (remaining=30727)
[2026-06-08T08:55:45] Filtering fusions with an e-value >=0.3 (remaining=8896)
[2026-06-08T08:55:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8944)
[2026-06-08T08:55:50] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8819)
[2026-06-08T08:55:51] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8819)
[2026-06-08T08:55:52] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6245)
[2026-06-08T08:55:57] Searching for fusions with spliced split reads (remaining=6360)
[2026-06-08T08:56:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=3988)
[2026-06-08T08:56:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3948)
[2026-06-08T08:56:04] Searching for fusions with >=4 spliced events (remaining=4782)
[2026-06-08T08:56:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1991)
[2026-06-08T08:56:20] Filtering fusions with anchors <=23nt (remaining=1644)
[2026-06-08T08:56:21] Filtering end-to-end fusions with low support (remaining=1589)
[2026-06-08T08:56:21] Filtering fusions with no coverage around the breakpoints (remaining=1551)
[2026-06-08T08:56:22] Indexing gene sequences 
[2026-06-08T08:56:27] Filtering genes with >=30% identity (remaining=449)
[2026-06-08T08:56:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=188)
[2026-06-08T08:56:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=135)
[2026-06-08T08:56:34] Searching for additional isoforms (remaining=187)
[2026-06-08T08:56:35] Assigning confidence scores to events 
[2026-06-08T08:56:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:56:38] Writing fusions to file 'aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:56:40] Writing discarded fusions to file 'aih-tih-sc-2a8dd7-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:57:09] Freeing resources
[2026-06-08T08:57:26] Done (elapsed time=00:11:30, CPU time=00:11:28, peak memory=15.3gb)