[2026-06-08T08:46:15] Launching Arriba 2.4.0
[2026-06-08T08:46:15] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:24] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:46:28] Reading chimeric alignments from 'aih-tih-sc-3a9c1f-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=12066474)
[2026-06-08T08:52:57] Marking multi-mapping alignments (marked=8525982)
[2026-06-08T08:53:02] Detecting strandedness (reverse)
[2026-06-08T08:53:02] Assigning strands to alignments 
[2026-06-08T08:53:05] Annotating alignments 
[2026-06-08T08:53:46] Filtering duplicates (remaining=3772403)
[2026-06-08T08:53:53] 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=3410991)
[2026-06-08T08:53:55] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3410991)
[2026-06-08T08:53:58] Filtering viral contigs with expression lower than the top 5 (remaining=3410991)
[2026-06-08T08:54:03] Filtering viral contigs with less than 5% coverage (remaining=3410991)
[2026-06-08T08:54:06] Estimating fragment length (mate gap mean=-84.8018, mate gap stddev=28.4642, read length mean=123.008)
[2026-06-08T08:54:06] Filtering read-through fragments with a distance <=10000bp (remaining=3254173)
[2026-06-08T08:54:09] Filtering inconsistently clipped mates (remaining=3189507)
[2026-06-08T08:54:12] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3057765)
[2026-06-08T08:54:15] Filtering fragments with small insert size (remaining=3056975)
[2026-06-08T08:54:18] Filtering alignments with long gaps (remaining=3056975)
[2026-06-08T08:54:21] Filtering fragments with both mates in the same gene (remaining=3056360)
[2026-06-08T08:54:24] Filtering fusions arising from hairpin structures (remaining=2902226)
[2026-06-08T08:54:27] Filtering reads with a mismatch p-value <=0.01 (remaining=1224699)
[2026-06-08T08:54:37] Filtering reads with low entropy (k-mer content >=60%) (remaining=372659)
[2026-06-08T08:54:46] Finding fusions and counting supporting reads (total=318501)
[2026-06-08T08:55:04] Merging adjacent fusion breakpoints (remaining=315584)
[2026-06-08T08:55:05] Filtering multi-mapping fusions by alignment score and read support (remaining=175125)
[2026-06-08T08:55:43] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:55:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=174043)
[2026-06-08T08:55:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=102027)
[2026-06-08T08:55:50] Filtering fusions with <2 supporting reads (remaining=10938)
[2026-06-08T08:55:51] Filtering fusions with an e-value >=0.3 (remaining=2816)
[2026-06-08T08:55:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2844)
[2026-06-08T08:55:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2776)
[2026-06-08T08:55:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2776)
[2026-06-08T08:55:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2663)
[2026-06-08T08:56:02] Searching for fusions with spliced split reads (remaining=2800)
[2026-06-08T08:56:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=2047)
[2026-06-08T08:56:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2032)
[2026-06-08T08:56:08] Searching for fusions with >=4 spliced events (remaining=2240)
[2026-06-08T08:56:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=770)
[2026-06-08T08:56:23] Filtering fusions with anchors <=23nt (remaining=602)
[2026-06-08T08:56:23] Filtering end-to-end fusions with low support (remaining=578)
[2026-06-08T08:56:24] Filtering fusions with no coverage around the breakpoints (remaining=565)
[2026-06-08T08:56:24] Indexing gene sequences 
[2026-06-08T08:56:28] Filtering genes with >=30% identity (remaining=183)
[2026-06-08T08:56:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=60)
[2026-06-08T08:56:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=60)
[2026-06-08T08:56:31] Searching for additional isoforms (remaining=70)
[2026-06-08T08:56:32] Assigning confidence scores to events 
[2026-06-08T08:56:34] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:56:34] Writing fusions to file 'aih-tih-sc-3a9c1f-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:56:35] Writing discarded fusions to file 'aih-tih-sc-3a9c1f-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:56:57] Freeing resources
[2026-06-08T08:57:17] Done (elapsed time=00:11:02, CPU time=00:11:00, peak memory=16.5gb)