[2026-06-08T08:23:59] Launching Arriba 2.4.0
[2026-06-08T08:23:59] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:24:13] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:24:18] Reading chimeric alignments from 'aih-tih-sc-6064dc-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=7487736)
[2026-06-08T08:28:40] Marking multi-mapping alignments (marked=5194863)
[2026-06-08T08:28:43] Detecting strandedness (reverse)
[2026-06-08T08:28:43] Assigning strands to alignments 
[2026-06-08T08:28:44] Annotating alignments 
[2026-06-08T08:29:05] Filtering duplicates (remaining=2559752)
[2026-06-08T08:29:08] 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=2172934)
[2026-06-08T08:29:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2172934)
[2026-06-08T08:29:11] Filtering viral contigs with expression lower than the top 5 (remaining=2172934)
[2026-06-08T08:29:13] Filtering viral contigs with less than 5% coverage (remaining=2172934)
[2026-06-08T08:29:14] Estimating fragment length (mate gap mean=-83.1621, mate gap stddev=30.9047, read length mean=127.266)
[2026-06-08T08:29:14] Filtering read-through fragments with a distance <=10000bp (remaining=2090759)
[2026-06-08T08:29:16] Filtering inconsistently clipped mates (remaining=2058005)
[2026-06-08T08:29:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1991481)
[2026-06-08T08:29:19] Filtering fragments with small insert size (remaining=1990965)
[2026-06-08T08:29:20] Filtering alignments with long gaps (remaining=1990965)
[2026-06-08T08:29:21] Filtering fragments with both mates in the same gene (remaining=1990574)
[2026-06-08T08:29:22] Filtering fusions arising from hairpin structures (remaining=1907108)
[2026-06-08T08:29:24] Filtering reads with a mismatch p-value <=0.01 (remaining=826442)
[2026-06-08T08:29:28] Filtering reads with low entropy (k-mer content >=60%) (remaining=257229)
[2026-06-08T08:29:33] Finding fusions and counting supporting reads (total=207783)
[2026-06-08T08:29:41] Merging adjacent fusion breakpoints (remaining=206581)
[2026-06-08T08:29:41] Filtering multi-mapping fusions by alignment score and read support (remaining=132415)
[2026-06-08T08:29:59] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:30:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=131295)
[2026-06-08T08:30:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=76594)
[2026-06-08T08:30:02] Filtering fusions with <2 supporting reads (remaining=11319)
[2026-06-08T08:30:02] Filtering fusions with an e-value >=0.3 (remaining=5225)
[2026-06-08T08:30:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5249)
[2026-06-08T08:30:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5221)
[2026-06-08T08:30:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5221)
[2026-06-08T08:30:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2199)
[2026-06-08T08:30:08] Searching for fusions with spliced split reads (remaining=2324)
[2026-06-08T08:30:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=1632)
[2026-06-08T08:30:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1609)
[2026-06-08T08:30:11] Searching for fusions with >=4 spliced events (remaining=1738)
[2026-06-08T08:30:11] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=460)
[2026-06-08T08:30:25] Filtering fusions with anchors <=23nt (remaining=349)
[2026-06-08T08:30:25] Filtering end-to-end fusions with low support (remaining=329)
[2026-06-08T08:30:26] Filtering fusions with no coverage around the breakpoints (remaining=320)
[2026-06-08T08:30:26] Indexing gene sequences 
[2026-06-08T08:30:28] Filtering genes with >=30% identity (remaining=117)
[2026-06-08T08:30:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=69)
[2026-06-08T08:30:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=69)
[2026-06-08T08:30:30] Searching for additional isoforms (remaining=79)
[2026-06-08T08:30:30] Assigning confidence scores to events 
[2026-06-08T08:30:31] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:30:32] Writing fusions to file 'aih-tih-sc-6064dc-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:30:32] Writing discarded fusions to file 'aih-tih-sc-6064dc-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:30:42] Freeing resources
[2026-06-08T08:30:53] Done (elapsed time=00:06:54, CPU time=00:06:53, peak memory=11.8gb)