[2026-06-08T08:47:09] Launching Arriba 2.4.0
[2026-06-08T08:47:09] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:22] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:27] Reading chimeric alignments from 'aih-tih-sc-8b4971-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11675480)
[2026-06-08T08:55:17] Marking multi-mapping alignments (marked=7659158)
[2026-06-08T08:55:23] Detecting strandedness (reverse)
[2026-06-08T08:55:23] Assigning strands to alignments 
[2026-06-08T08:55:25] Annotating alignments 
[2026-06-08T08:56:04] Filtering duplicates (remaining=6371253)
[2026-06-08T08:56:13] 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=6072037)
[2026-06-08T08:56:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6072037)
[2026-06-08T08:56:18] Filtering viral contigs with expression lower than the top 5 (remaining=6072037)
[2026-06-08T08:56:23] Filtering viral contigs with less than 5% coverage (remaining=6072037)
[2026-06-08T08:56:26] Estimating fragment length (mate gap mean=-88.5835, mate gap stddev=27.3041, read length mean=130.456)
[2026-06-08T08:56:26] Filtering read-through fragments with a distance <=10000bp (remaining=5755644)
[2026-06-08T08:56:29] Filtering inconsistently clipped mates (remaining=5674073)
[2026-06-08T08:56:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5520518)
[2026-06-08T08:56:38] Filtering fragments with small insert size (remaining=5519953)
[2026-06-08T08:56:40] Filtering alignments with long gaps (remaining=5519953)
[2026-06-08T08:56:43] Filtering fragments with both mates in the same gene (remaining=5518919)
[2026-06-08T08:56:45] Filtering fusions arising from hairpin structures (remaining=5292493)
[2026-06-08T08:56:48] Filtering reads with a mismatch p-value <=0.01 (remaining=2456054)
[2026-06-08T08:57:02] Filtering reads with low entropy (k-mer content >=60%) (remaining=825292)
[2026-06-08T08:57:11] Finding fusions and counting supporting reads (total=626383)
[2026-06-08T08:57:29] Merging adjacent fusion breakpoints (remaining=619114)
[2026-06-08T08:57:31] Filtering multi-mapping fusions by alignment score and read support (remaining=369547)
[2026-06-08T08:58:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=368106)
[2026-06-08T08:58:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=231226)
[2026-06-08T08:58:19] Filtering fusions with <2 supporting reads (remaining=26785)
[2026-06-08T08:58:20] Filtering fusions with an e-value >=0.3 (remaining=6645)
[2026-06-08T08:58:21] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6697)
[2026-06-08T08:58:25] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6579)
[2026-06-08T08:58:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6579)
[2026-06-08T08:58:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5868)
[2026-06-08T08:58:33] Searching for fusions with spliced split reads (remaining=5966)
[2026-06-08T08:58:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=4053)
[2026-06-08T08:58:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3991)
[2026-06-08T08:58:41] Searching for fusions with >=4 spliced events (remaining=4622)
[2026-06-08T08:58:42] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1914)
[2026-06-08T08:58:58] Filtering fusions with anchors <=23nt (remaining=1555)
[2026-06-08T08:58:59] Filtering end-to-end fusions with low support (remaining=1511)
[2026-06-08T08:59:00] Filtering fusions with no coverage around the breakpoints (remaining=1474)
[2026-06-08T08:59:00] Indexing gene sequences 
[2026-06-08T08:59:07] Filtering genes with >=30% identity (remaining=536)
[2026-06-08T08:59:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=314)
[2026-06-08T08:59:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=249)
[2026-06-08T08:59:19] Searching for additional isoforms (remaining=306)
[2026-06-08T08:59:21] Assigning confidence scores to events 
[2026-06-08T08:59:24] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:24] Writing fusions to file 'aih-tih-sc-8b4971-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:27] Writing discarded fusions to file 'aih-tih-sc-8b4971-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:56] Freeing resources
[2026-06-08T09:00:14] Done (elapsed time=00:13:05, CPU time=00:13:03, peak memory=16gb)