[2026-06-08T08:48:29] Launching Arriba 2.4.0
[2026-06-08T08:48:29] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:42] Reading chimeric alignments from 'aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=8946274)
[2026-06-08T08:55:19] Marking multi-mapping alignments (marked=5510631)
[2026-06-08T08:55:23] Detecting strandedness (reverse)
[2026-06-08T08:55:23] Assigning strands to alignments 
[2026-06-08T08:55:25] Annotating alignments 
[2026-06-08T08:55:56] Filtering duplicates (remaining=5629034)
[2026-06-08T08:56:02] 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=5362998)
[2026-06-08T08:56:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5362998)
[2026-06-08T08:56:06] Filtering viral contigs with expression lower than the top 5 (remaining=5362998)
[2026-06-08T08:56:11] Filtering viral contigs with less than 5% coverage (remaining=5362998)
[2026-06-08T08:56:13] Estimating fragment length (mate gap mean=-85.8317, mate gap stddev=30.6699, read length mean=135.127)
[2026-06-08T08:56:13] Filtering read-through fragments with a distance <=10000bp (remaining=5026773)
[2026-06-08T08:56:15] Filtering inconsistently clipped mates (remaining=4942791)
[2026-06-08T08:56:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4814467)
[2026-06-08T08:56:22] Filtering fragments with small insert size (remaining=4813625)
[2026-06-08T08:56:24] Filtering alignments with long gaps (remaining=4813624)
[2026-06-08T08:56:26] Filtering fragments with both mates in the same gene (remaining=4812678)
[2026-06-08T08:56:28] Filtering fusions arising from hairpin structures (remaining=4518270)
[2026-06-08T08:56:31] Filtering reads with a mismatch p-value <=0.01 (remaining=2139207)
[2026-06-08T08:56:42] Filtering reads with low entropy (k-mer content >=60%) (remaining=949861)
[2026-06-08T08:56:53] Finding fusions and counting supporting reads (total=702429)
[2026-06-08T08:57:09] Merging adjacent fusion breakpoints (remaining=696392)
[2026-06-08T08:57:10] Filtering multi-mapping fusions by alignment score and read support (remaining=443561)
[2026-06-08T08:57:40] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=440083)
[2026-06-08T08:57:47] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=240399)
[2026-06-08T08:57:49] Filtering fusions with <2 supporting reads (remaining=37672)
[2026-06-08T08:57:49] Filtering fusions with an e-value >=0.3 (remaining=13986)
[2026-06-08T08:57:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14056)
[2026-06-08T08:57:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13988)
[2026-06-08T08:57:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13988)
[2026-06-08T08:57:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7781)
[2026-06-08T08:58:00] Searching for fusions with spliced split reads (remaining=7923)
[2026-06-08T08:58:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=4606)
[2026-06-08T08:58:05] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4539)
[2026-06-08T08:58:06] Searching for fusions with >=4 spliced events (remaining=5366)
[2026-06-08T08:58:07] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1849)
[2026-06-08T08:58:21] Filtering fusions with anchors <=23nt (remaining=1482)
[2026-06-08T08:58:22] Filtering end-to-end fusions with low support (remaining=1436)
[2026-06-08T08:58:23] Filtering fusions with no coverage around the breakpoints (remaining=1406)
[2026-06-08T08:58:23] Indexing gene sequences 
[2026-06-08T08:58:28] Filtering genes with >=30% identity (remaining=396)
[2026-06-08T08:58:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=171)
[2026-06-08T08:58:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=167)
[2026-06-08T08:58:37] Searching for additional isoforms (remaining=217)
[2026-06-08T08:58:38] Assigning confidence scores to events 
[2026-06-08T08:58:41] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:41] Writing fusions to file 'aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:58:43] Writing discarded fusions to file 'aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:12] Freeing resources
[2026-06-08T08:59:27] Done (elapsed time=00:10:58, CPU time=00:10:57, peak memory=13.6gb)