[2026-06-08T08:28:02] Launching Arriba 2.4.0
[2026-06-08T08:28:02] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:28:11] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:28:15] Reading chimeric alignments from 'aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=6345440)
[2026-06-08T08:32:22] Marking multi-mapping alignments (marked=4019705)
[2026-06-08T08:32:24] Detecting strandedness (reverse)
[2026-06-08T08:32:24] Assigning strands to alignments 
[2026-06-08T08:32:25] Annotating alignments 
[2026-06-08T08:32:46] Filtering duplicates (remaining=3247219)
[2026-06-08T08:32:49] 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=3091257)
[2026-06-08T08:32:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3091257)
[2026-06-08T08:32:52] Filtering viral contigs with expression lower than the top 5 (remaining=3091257)
[2026-06-08T08:32:54] Filtering viral contigs with less than 5% coverage (remaining=3091257)
[2026-06-08T08:32:56] Estimating fragment length (mate gap mean=-84.0461, mate gap stddev=29.5269, read length mean=128.949)
[2026-06-08T08:32:56] Filtering read-through fragments with a distance <=10000bp (remaining=2928833)
[2026-06-08T08:32:57] Filtering inconsistently clipped mates (remaining=2871084)
[2026-06-08T08:32:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2789849)
[2026-06-08T08:33:01] Filtering fragments with small insert size (remaining=2789254)
[2026-06-08T08:33:02] Filtering alignments with long gaps (remaining=2789254)
[2026-06-08T08:33:03] Filtering fragments with both mates in the same gene (remaining=2788665)
[2026-06-08T08:33:04] Filtering fusions arising from hairpin structures (remaining=2617221)
[2026-06-08T08:33:06] Filtering reads with a mismatch p-value <=0.01 (remaining=1223991)
[2026-06-08T08:33:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=444065)
[2026-06-08T08:33:18] Finding fusions and counting supporting reads (total=357077)
[2026-06-08T08:33:27] Merging adjacent fusion breakpoints (remaining=354570)
[2026-06-08T08:33:28] Filtering multi-mapping fusions by alignment score and read support (remaining=221574)
[2026-06-08T08:33:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:33:52] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=220050)
[2026-06-08T08:33:52] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=121130)
[2026-06-08T08:33:53] Filtering fusions with <2 supporting reads (remaining=17493)
[2026-06-08T08:33:53] Filtering fusions with an e-value >=0.3 (remaining=5648)
[2026-06-08T08:33:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5692)
[2026-06-08T08:33:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5658)
[2026-06-08T08:33:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5658)
[2026-06-08T08:33:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4060)
[2026-06-08T08:34:00] Searching for fusions with spliced split reads (remaining=4132)
[2026-06-08T08:34:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=2731)
[2026-06-08T08:34:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2692)
[2026-06-08T08:34:04] Searching for fusions with >=4 spliced events (remaining=2973)
[2026-06-08T08:34:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=820)
[2026-06-08T08:34:17] Filtering fusions with anchors <=23nt (remaining=683)
[2026-06-08T08:34:17] Filtering end-to-end fusions with low support (remaining=659)
[2026-06-08T08:34:17] Filtering fusions with no coverage around the breakpoints (remaining=651)
[2026-06-08T08:34:18] Indexing gene sequences 
[2026-06-08T08:34:21] Filtering genes with >=30% identity (remaining=220)
[2026-06-08T08:34:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=125)
[2026-06-08T08:34:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=125)
[2026-06-08T08:34:24] Searching for additional isoforms (remaining=145)
[2026-06-08T08:34:25] Assigning confidence scores to events 
[2026-06-08T08:34:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:34:26] Writing fusions to file 'aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:34:27] Writing discarded fusions to file 'aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:34:43] Freeing resources
[2026-06-08T08:34:53] Done (elapsed time=00:06:51, CPU time=00:06:50, peak memory=10.7gb)