[2026-06-08T08:51:49] Launching Arriba 2.4.0
[2026-06-08T08:51:49] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:51:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:03] Reading chimeric alignments from 'aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9766272)
[2026-06-08T08:59:25] Marking multi-mapping alignments (marked=6245319)
[2026-06-08T08:59:29] Detecting strandedness (reverse)
[2026-06-08T08:59:29] Assigning strands to alignments 
[2026-06-08T08:59:32] Annotating alignments 
[2026-06-08T09:00:12] Filtering duplicates (remaining=5969618)
[2026-06-08T09:00:20] 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=5703278)
[2026-06-08T09:00:23] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5703278)
[2026-06-08T09:00:25] Filtering viral contigs with expression lower than the top 5 (remaining=5703278)
[2026-06-08T09:00:30] Filtering viral contigs with less than 5% coverage (remaining=5703278)
[2026-06-08T09:00:32] Estimating fragment length (mate gap mean=-86.6214, mate gap stddev=29.8932, read length mean=135.426)
[2026-06-08T09:00:32] Filtering read-through fragments with a distance <=10000bp (remaining=5387676)
[2026-06-08T09:00:34] Filtering inconsistently clipped mates (remaining=5294984)
[2026-06-08T09:00:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5146199)
[2026-06-08T09:00:41] Filtering fragments with small insert size (remaining=5145544)
[2026-06-08T09:00:43] Filtering alignments with long gaps (remaining=5145544)
[2026-06-08T09:00:45] Filtering fragments with both mates in the same gene (remaining=5144535)
[2026-06-08T09:00:48] Filtering fusions arising from hairpin structures (remaining=4806784)
[2026-06-08T09:00:50] Filtering reads with a mismatch p-value <=0.01 (remaining=2359280)
[2026-06-08T09:01:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=961632)
[2026-06-08T09:01:16] Finding fusions and counting supporting reads (total=717383)
[2026-06-08T09:01:36] Merging adjacent fusion breakpoints (remaining=712256)
[2026-06-08T09:01:38] Filtering multi-mapping fusions by alignment score and read support (remaining=425995)
[2026-06-08T09:02:18] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:02:25] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=420951)
[2026-06-08T09:02:26] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=246479)
[2026-06-08T09:02:28] Filtering fusions with <2 supporting reads (remaining=35110)
[2026-06-08T09:02:29] Filtering fusions with an e-value >=0.3 (remaining=14351)
[2026-06-08T09:02:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14402)
[2026-06-08T09:02:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14276)
[2026-06-08T09:02:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14276)
[2026-06-08T09:02:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7180)
[2026-06-08T09:02:45] Searching for fusions with spliced split reads (remaining=7212)
[2026-06-08T09:02:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=4051)
[2026-06-08T09:02:59] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4015)
[2026-06-08T09:03:00] Searching for fusions with >=4 spliced events (remaining=4810)
[2026-06-08T09:03:02] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2048)
[2026-06-08T09:03:18] Filtering fusions with anchors <=23nt (remaining=1660)
[2026-06-08T09:03:19] Filtering end-to-end fusions with low support (remaining=1597)
[2026-06-08T09:03:20] Filtering fusions with no coverage around the breakpoints (remaining=1541)
[2026-06-08T09:03:21] Indexing gene sequences 
[2026-06-08T09:03:26] Filtering genes with >=30% identity (remaining=448)
[2026-06-08T09:03:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=213)
[2026-06-08T09:03:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=183)
[2026-06-08T09:03:34] Searching for additional isoforms (remaining=235)
[2026-06-08T09:03:35] Assigning confidence scores to events 
[2026-06-08T09:03:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:03:39] Writing fusions to file 'aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:03:40] Writing discarded fusions to file 'aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:04:14] Freeing resources
[2026-06-08T09:04:42] Done (elapsed time=00:12:53, CPU time=00:12:52, peak memory=14.3gb)