[2026-06-08T08:48:41] Launching Arriba 2.4.0
[2026-06-08T08:48:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:54] Reading chimeric alignments from 'aih-tih-sc-538ae3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10195403)
[2026-06-08T08:55:57] Marking multi-mapping alignments (marked=6896908)
[2026-06-08T08:56:02] Detecting strandedness (reverse)
[2026-06-08T08:56:02] Assigning strands to alignments 
[2026-06-08T08:56:04] Annotating alignments 
[2026-06-08T08:56:38] Filtering duplicates (remaining=7123111)
[2026-06-08T08:56:46] 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=6705797)
[2026-06-08T08:56:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6705797)
[2026-06-08T08:56:50] Filtering viral contigs with expression lower than the top 5 (remaining=6705797)
[2026-06-08T08:56:55] Filtering viral contigs with less than 5% coverage (remaining=6705797)
[2026-06-08T08:56:58] Estimating fragment length (mate gap mean=-85.04, mate gap stddev=29.1752, read length mean=128.69)
[2026-06-08T08:56:58] Filtering read-through fragments with a distance <=10000bp (remaining=6181379)
[2026-06-08T08:57:00] Filtering inconsistently clipped mates (remaining=6060108)
[2026-06-08T08:57:02] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5896592)
[2026-06-08T08:57:07] Filtering fragments with small insert size (remaining=5895691)
[2026-06-08T08:57:09] Filtering alignments with long gaps (remaining=5895691)
[2026-06-08T08:57:11] Filtering fragments with both mates in the same gene (remaining=5894595)
[2026-06-08T08:57:13] Filtering fusions arising from hairpin structures (remaining=5468322)
[2026-06-08T08:57:16] Filtering reads with a mismatch p-value <=0.01 (remaining=2448477)
[2026-06-08T08:57:30] Filtering reads with low entropy (k-mer content >=60%) (remaining=1246555)
[2026-06-08T08:57:42] Finding fusions and counting supporting reads (total=954628)
[2026-06-08T08:58:00] Merging adjacent fusion breakpoints (remaining=942044)
[2026-06-08T08:58:02] Filtering multi-mapping fusions by alignment score and read support (remaining=567973)
[2026-06-08T08:58:37] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:45] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=565935)
[2026-06-08T08:58:46] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=328220)
[2026-06-08T08:58:47] Filtering fusions with <2 supporting reads (remaining=34986)
[2026-06-08T08:58:48] Filtering fusions with an e-value >=0.3 (remaining=9646)
[2026-06-08T08:58:49] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9705)
[2026-06-08T08:58:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9550)
[2026-06-08T08:58:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9550)
[2026-06-08T08:58:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8074)
[2026-06-08T08:59:01] Searching for fusions with spliced split reads (remaining=8102)
[2026-06-08T08:59:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=4701)
[2026-06-08T08:59:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4649)
[2026-06-08T08:59:08] Searching for fusions with >=4 spliced events (remaining=5676)
[2026-06-08T08:59:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2488)
[2026-06-08T08:59:28] Filtering fusions with anchors <=23nt (remaining=1886)
[2026-06-08T08:59:29] Filtering end-to-end fusions with low support (remaining=1826)
[2026-06-08T08:59:29] Filtering fusions with no coverage around the breakpoints (remaining=1793)
[2026-06-08T08:59:30] Indexing gene sequences 
[2026-06-08T08:59:37] Filtering genes with >=30% identity (remaining=538)
[2026-06-08T08:59:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=212)
[2026-06-08T08:59:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=205)
[2026-06-08T08:59:44] Searching for additional isoforms (remaining=253)
[2026-06-08T08:59:46] Assigning confidence scores to events 
[2026-06-08T08:59:50] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:50] Writing fusions to file 'aih-tih-sc-538ae3-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:52] Writing discarded fusions to file 'aih-tih-sc-538ae3-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:25] Freeing resources
[2026-06-08T09:00:41] Done (elapsed time=00:12:00, CPU time=00:11:59, peak memory=15.1gb)