[2026-06-08T08:26:54] Launching Arriba 2.4.0
[2026-06-08T08:26:54] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:27:07] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:10] Reading chimeric alignments from 'aih-tih-sc-6473fb-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10685354)
[2026-06-08T08:32:26] Marking multi-mapping alignments (marked=7028907)
[2026-06-08T08:32:30] Detecting strandedness (reverse)
[2026-06-08T08:32:30] Assigning strands to alignments 
[2026-06-08T08:32:32] Annotating alignments 
[2026-06-08T08:33:02] Filtering duplicates (remaining=3729998)
[2026-06-08T08:33:07] 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=3492676)
[2026-06-08T08:33:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3492676)
[2026-06-08T08:33:11] Filtering viral contigs with expression lower than the top 5 (remaining=3492676)
[2026-06-08T08:33:15] Filtering viral contigs with less than 5% coverage (remaining=3492676)
[2026-06-08T08:33:17] Estimating fragment length (mate gap mean=-86.5179, mate gap stddev=27.2997, read length mean=126.664)
[2026-06-08T08:33:18] Filtering read-through fragments with a distance <=10000bp (remaining=3357792)
[2026-06-08T08:33:20] Filtering inconsistently clipped mates (remaining=3298799)
[2026-06-08T08:33:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3182618)
[2026-06-08T08:33:24] Filtering fragments with small insert size (remaining=3181926)
[2026-06-08T08:33:26] Filtering alignments with long gaps (remaining=3181926)
[2026-06-08T08:33:28] Filtering fragments with both mates in the same gene (remaining=3181087)
[2026-06-08T08:33:30] Filtering fusions arising from hairpin structures (remaining=3035019)
[2026-06-08T08:33:32] Filtering reads with a mismatch p-value <=0.01 (remaining=1266583)
[2026-06-08T08:33:40] Filtering reads with low entropy (k-mer content >=60%) (remaining=384481)
[2026-06-08T08:33:47] Finding fusions and counting supporting reads (total=307822)
[2026-06-08T08:34:00] Merging adjacent fusion breakpoints (remaining=304770)
[2026-06-08T08:34:01] Filtering multi-mapping fusions by alignment score and read support (remaining=178224)
[2026-06-08T08:34:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:34:33] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=177329)
[2026-06-08T08:34:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=102880)
[2026-06-08T08:34:34] Filtering fusions with <2 supporting reads (remaining=12993)
[2026-06-08T08:34:34] Filtering fusions with an e-value >=0.3 (remaining=3312)
[2026-06-08T08:34:35] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3346)
[2026-06-08T08:34:37] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3279)
[2026-06-08T08:34:38] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3279)
[2026-06-08T08:34:39] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3076)
[2026-06-08T08:34:43] Searching for fusions with spliced split reads (remaining=3218)
[2026-06-08T08:34:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=2293)
[2026-06-08T08:34:47] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2259)
[2026-06-08T08:34:47] Searching for fusions with >=4 spliced events (remaining=2493)
[2026-06-08T08:34:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=697)
[2026-06-08T08:35:02] Filtering fusions with anchors <=23nt (remaining=596)
[2026-06-08T08:35:02] Filtering end-to-end fusions with low support (remaining=584)
[2026-06-08T08:35:03] Filtering fusions with no coverage around the breakpoints (remaining=565)
[2026-06-08T08:35:03] Indexing gene sequences 
[2026-06-08T08:35:06] Filtering genes with >=30% identity (remaining=215)
[2026-06-08T08:35:07] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=127)
[2026-06-08T08:35:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=124)
[2026-06-08T08:35:09] Searching for additional isoforms (remaining=136)
[2026-06-08T08:35:10] Assigning confidence scores to events 
[2026-06-08T08:35:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:35:12] Writing fusions to file 'aih-tih-sc-6473fb-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:35:13] Writing discarded fusions to file 'aih-tih-sc-6473fb-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:35:29] Freeing resources
[2026-06-08T08:35:44] Done (elapsed time=00:08:50, CPU time=00:08:49, peak memory=14.9gb)