[2026-06-08T08:55:19] Launching Arriba 2.4.0
[2026-06-08T08:55:19] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:55:32] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:55:35] Reading chimeric alignments from 'aih-tih-sc-2798bb-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10455474)
[2026-06-08T09:02:24] Marking multi-mapping alignments (marked=6706981)
[2026-06-08T09:02:28] Detecting strandedness (reverse)
[2026-06-08T09:02:28] Assigning strands to alignments 
[2026-06-08T09:02:29] Annotating alignments 
[2026-06-08T09:03:00] Filtering duplicates (remaining=5943485)
[2026-06-08T09:03:05] 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=5673848)
[2026-06-08T09:03:07] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5673848)
[2026-06-08T09:03:09] Filtering viral contigs with expression lower than the top 5 (remaining=5673848)
[2026-06-08T09:03:13] Filtering viral contigs with less than 5% coverage (remaining=5673848)
[2026-06-08T09:03:15] Estimating fragment length (mate gap mean=-87.3405, mate gap stddev=28.6136, read length mean=133.09)
[2026-06-08T09:03:15] Filtering read-through fragments with a distance <=10000bp (remaining=5324148)
[2026-06-08T09:03:17] Filtering inconsistently clipped mates (remaining=5240657)
[2026-06-08T09:03:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5108247)
[2026-06-08T09:03:23] Filtering fragments with small insert size (remaining=5107633)
[2026-06-08T09:03:24] Filtering alignments with long gaps (remaining=5107633)
[2026-06-08T09:03:26] Filtering fragments with both mates in the same gene (remaining=5106805)
[2026-06-08T09:03:28] Filtering fusions arising from hairpin structures (remaining=4835975)
[2026-06-08T09:03:30] Filtering reads with a mismatch p-value <=0.01 (remaining=2257330)
[2026-06-08T09:03:42] Filtering reads with low entropy (k-mer content >=60%) (remaining=935729)
[2026-06-08T09:03:52] Finding fusions and counting supporting reads (total=717912)
[2026-06-08T09:04:07] Merging adjacent fusion breakpoints (remaining=711450)
[2026-06-08T09:04:08] Filtering multi-mapping fusions by alignment score and read support (remaining=443057)
[2026-06-08T09:04:36] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:04:42] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=440954)
[2026-06-08T09:04:42] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=240384)
[2026-06-08T09:04:43] Filtering fusions with <2 supporting reads (remaining=32906)
[2026-06-08T09:04:44] Filtering fusions with an e-value >=0.3 (remaining=9235)
[2026-06-08T09:04:44] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9280)
[2026-06-08T09:04:48] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9223)
[2026-06-08T09:04:48] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9224)
[2026-06-08T09:04:50] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7485)
[2026-06-08T09:04:54] Searching for fusions with spliced split reads (remaining=7622)
[2026-06-08T09:04:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=4756)
[2026-06-08T09:04:59] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4709)
[2026-06-08T09:05:00] Searching for fusions with >=4 spliced events (remaining=5634)
[2026-06-08T09:05:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2090)
[2026-06-08T09:05:15] Filtering fusions with anchors <=23nt (remaining=1670)
[2026-06-08T09:05:16] Filtering end-to-end fusions with low support (remaining=1617)
[2026-06-08T09:05:16] Filtering fusions with no coverage around the breakpoints (remaining=1579)
[2026-06-08T09:05:17] Indexing gene sequences 
[2026-06-08T09:05:22] Filtering genes with >=30% identity (remaining=460)
[2026-06-08T09:05:24] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=192)
[2026-06-08T09:05:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=187)
[2026-06-08T09:05:28] Searching for additional isoforms (remaining=225)
[2026-06-08T09:05:29] Assigning confidence scores to events 
[2026-06-08T09:05:32] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:05:32] Writing fusions to file 'aih-tih-sc-2798bb-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:05:33] Writing discarded fusions to file 'aih-tih-sc-2798bb-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:05:58] Freeing resources
[2026-06-08T09:06:14] Done (elapsed time=00:10:55, CPU time=00:10:54, peak memory=15.1gb)