[2026-06-08T08:46:39] Launching Arriba 2.4.0
[2026-06-08T08:46:39] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:00] Reading chimeric alignments from 'aih-tih-sc-e33b0b-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9632084)
[2026-06-08T08:55:20] Marking multi-mapping alignments (marked=6155961)
[2026-06-08T08:55:25] Detecting strandedness (reverse)
[2026-06-08T08:55:25] Assigning strands to alignments 
[2026-06-08T08:55:27] Annotating alignments 
[2026-06-08T08:55:59] Filtering duplicates (remaining=4504379)
[2026-06-08T08:56:05] 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=4221469)
[2026-06-08T08:56:07] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4221469)
[2026-06-08T08:56:09] Filtering viral contigs with expression lower than the top 5 (remaining=4221469)
[2026-06-08T08:56:14] Filtering viral contigs with less than 5% coverage (remaining=4221469)
[2026-06-08T08:56:16] Estimating fragment length (mate gap mean=-85.3777, mate gap stddev=30.2128, read length mean=130.973)
[2026-06-08T08:56:16] Filtering read-through fragments with a distance <=10000bp (remaining=4038003)
[2026-06-08T08:56:18] Filtering inconsistently clipped mates (remaining=3972581)
[2026-06-08T08:56:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3863637)
[2026-06-08T08:56:24] Filtering fragments with small insert size (remaining=3863039)
[2026-06-08T08:56:26] Filtering alignments with long gaps (remaining=3863039)
[2026-06-08T08:56:28] Filtering fragments with both mates in the same gene (remaining=3862204)
[2026-06-08T08:56:30] Filtering fusions arising from hairpin structures (remaining=3655137)
[2026-06-08T08:56:33] Filtering reads with a mismatch p-value <=0.01 (remaining=1610732)
[2026-06-08T08:56:44] Filtering reads with low entropy (k-mer content >=60%) (remaining=513947)
[2026-06-08T08:56:52] Finding fusions and counting supporting reads (total=399273)
[2026-06-08T08:57:07] Merging adjacent fusion breakpoints (remaining=396388)
[2026-06-08T08:57:08] Filtering multi-mapping fusions by alignment score and read support (remaining=256358)
[2026-06-08T08:57:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:46] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=254864)
[2026-06-08T08:57:47] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=143652)
[2026-06-08T08:57:47] Filtering fusions with <2 supporting reads (remaining=21472)
[2026-06-08T08:57:48] Filtering fusions with an e-value >=0.3 (remaining=9214)
[2026-06-08T08:57:48] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9262)
[2026-06-08T08:57:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9216)
[2026-06-08T08:57:52] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9216)
[2026-06-08T08:57:53] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3988)
[2026-06-08T08:57:57] Searching for fusions with spliced split reads (remaining=4091)
[2026-06-08T08:58:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=2614)
[2026-06-08T08:58:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2583)
[2026-06-08T08:58:03] Searching for fusions with >=4 spliced events (remaining=3013)
[2026-06-08T08:58:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1004)
[2026-06-08T08:58:17] Filtering fusions with anchors <=23nt (remaining=755)
[2026-06-08T08:58:17] Filtering end-to-end fusions with low support (remaining=727)
[2026-06-08T08:58:18] Filtering fusions with no coverage around the breakpoints (remaining=712)
[2026-06-08T08:58:18] Indexing gene sequences 
[2026-06-08T08:58:22] Filtering genes with >=30% identity (remaining=228)
[2026-06-08T08:58:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=123)
[2026-06-08T08:58:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=115)
[2026-06-08T08:58:26] Searching for additional isoforms (remaining=142)
[2026-06-08T08:58:27] Assigning confidence scores to events 
[2026-06-08T08:58:29] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:29] Writing fusions to file 'aih-tih-sc-e33b0b-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:58:30] Writing discarded fusions to file 'aih-tih-sc-e33b0b-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:58:52] Freeing resources
[2026-06-08T08:59:08] Done (elapsed time=00:12:29, CPU time=00:12:27, peak memory=13.9gb)