[2026-06-08T08:44:30] Launching Arriba 2.4.0
[2026-06-08T08:44:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:44:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:44:43] Reading chimeric alignments from 'aih-tih-sc-5b8b4a-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11209737)
[2026-06-08T08:51:26] Marking multi-mapping alignments (marked=7416045)
[2026-06-08T08:51:31] Detecting strandedness (reverse)
[2026-06-08T08:51:31] Assigning strands to alignments 
[2026-06-08T08:51:33] Annotating alignments 
[2026-06-08T08:52:11] Filtering duplicates (remaining=6684434)
[2026-06-08T08:52:18] 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=6207275)
[2026-06-08T08:52:20] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6207275)
[2026-06-08T08:52:22] Filtering viral contigs with expression lower than the top 5 (remaining=6207275)
[2026-06-08T08:52:27] Filtering viral contigs with less than 5% coverage (remaining=6207275)
[2026-06-08T08:52:29] Estimating fragment length (mate gap mean=-85.3004, mate gap stddev=28.3782, read length mean=124.722)
[2026-06-08T08:52:30] Filtering read-through fragments with a distance <=10000bp (remaining=5857238)
[2026-06-08T08:52:32] Filtering inconsistently clipped mates (remaining=5730130)
[2026-06-08T08:52:34] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5561796)
[2026-06-08T08:52:38] Filtering fragments with small insert size (remaining=5560225)
[2026-06-08T08:52:41] Filtering alignments with long gaps (remaining=5560224)
[2026-06-08T08:52:43] Filtering fragments with both mates in the same gene (remaining=5558807)
[2026-06-08T08:52:45] Filtering fusions arising from hairpin structures (remaining=5185320)
[2026-06-08T08:52:48] Filtering reads with a mismatch p-value <=0.01 (remaining=2128056)
[2026-06-08T08:53:02] Filtering reads with low entropy (k-mer content >=60%) (remaining=1037864)
[2026-06-08T08:53:12] Finding fusions and counting supporting reads (total=773176)
[2026-06-08T08:53:29] Merging adjacent fusion breakpoints (remaining=767215)
[2026-06-08T08:53:31] Filtering multi-mapping fusions by alignment score and read support (remaining=467335)
[2026-06-08T08:54:06] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:54:13] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=465319)
[2026-06-08T08:54:14] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=283002)
[2026-06-08T08:54:15] Filtering fusions with <2 supporting reads (remaining=36069)
[2026-06-08T08:54:16] Filtering fusions with an e-value >=0.3 (remaining=8657)
[2026-06-08T08:54:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8722)
[2026-06-08T08:54:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8653)
[2026-06-08T08:54:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8653)
[2026-06-08T08:54:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7144)
[2026-06-08T08:54:28] Searching for fusions with spliced split reads (remaining=7278)
[2026-06-08T08:54:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=4853)
[2026-06-08T08:54:35] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4779)
[2026-06-08T08:54:36] Searching for fusions with >=4 spliced events (remaining=5727)
[2026-06-08T08:54:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2076)
[2026-06-08T08:54:52] Filtering fusions with anchors <=23nt (remaining=1672)
[2026-06-08T08:54:53] Filtering end-to-end fusions with low support (remaining=1619)
[2026-06-08T08:54:53] Filtering fusions with no coverage around the breakpoints (remaining=1586)
[2026-06-08T08:54:54] Indexing gene sequences 
[2026-06-08T08:55:00] Filtering genes with >=30% identity (remaining=463)
[2026-06-08T08:55:03] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=206)
[2026-06-08T08:55:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=187)
[2026-06-08T08:55:07] Searching for additional isoforms (remaining=218)
[2026-06-08T08:55:08] Assigning confidence scores to events 
[2026-06-08T08:55:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:55:12] Writing fusions to file 'aih-tih-sc-5b8b4a-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:55:14] Writing discarded fusions to file 'aih-tih-sc-5b8b4a-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:55:45] Freeing resources
[2026-06-08T08:56:03] Done (elapsed time=00:11:33, CPU time=00:11:31, peak memory=16gb)