[2026-06-08T09:03:11] Launching Arriba 2.4.0
[2026-06-08T09:03:11] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:03:20] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:03:25] Reading chimeric alignments from 'aih-tih-sc-ea6ef3-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=12840662)
[2026-06-08T09:10:48] Marking multi-mapping alignments (marked=8644045)
[2026-06-08T09:10:54] Detecting strandedness (reverse)
[2026-06-08T09:10:54] Assigning strands to alignments 
[2026-06-08T09:10:56] Annotating alignments 
[2026-06-08T09:11:37] Filtering duplicates (remaining=7876477)
[2026-06-08T09:11:46] 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=7550437)
[2026-06-08T09:11:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7550437)
[2026-06-08T09:11:51] Filtering viral contigs with expression lower than the top 5 (remaining=7550437)
[2026-06-08T09:11:57] Filtering viral contigs with less than 5% coverage (remaining=7550437)
[2026-06-08T09:12:00] Estimating fragment length (mate gap mean=-85.9303, mate gap stddev=28.0655, read length mean=130.6)
[2026-06-08T09:12:00] Filtering read-through fragments with a distance <=10000bp (remaining=7061949)
[2026-06-08T09:12:03] Filtering inconsistently clipped mates (remaining=6969883)
[2026-06-08T09:12:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6780696)
[2026-06-08T09:12:11] Filtering fragments with small insert size (remaining=6780017)
[2026-06-08T09:12:13] Filtering alignments with long gaps (remaining=6780017)
[2026-06-08T09:12:16] Filtering fragments with both mates in the same gene (remaining=6779119)
[2026-06-08T09:12:19] Filtering fusions arising from hairpin structures (remaining=6478096)
[2026-06-08T09:12:22] Filtering reads with a mismatch p-value <=0.01 (remaining=3106307)
[2026-06-08T09:12:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=1098136)
[2026-06-08T09:12:51] Finding fusions and counting supporting reads (total=802198)
[2026-06-08T09:13:12] Merging adjacent fusion breakpoints (remaining=794188)
[2026-06-08T09:13:14] Filtering multi-mapping fusions by alignment score and read support (remaining=471796)
[2026-06-08T09:13:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:14:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=470465)
[2026-06-08T09:14:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=286736)
[2026-06-08T09:14:04] Filtering fusions with <2 supporting reads (remaining=29961)
[2026-06-08T09:14:05] Filtering fusions with an e-value >=0.3 (remaining=7107)
[2026-06-08T09:14:06] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7172)
[2026-06-08T09:14:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7083)
[2026-06-08T09:14:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7083)
[2026-06-08T09:14:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6663)
[2026-06-08T09:14:19] Searching for fusions with spliced split reads (remaining=6778)
[2026-06-08T09:14:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=4393)
[2026-06-08T09:14:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4364)
[2026-06-08T09:14:27] Searching for fusions with >=4 spliced events (remaining=5159)
[2026-06-08T09:14:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2224)
[2026-06-08T09:14:46] Filtering fusions with anchors <=23nt (remaining=1762)
[2026-06-08T09:14:46] Filtering end-to-end fusions with low support (remaining=1706)
[2026-06-08T09:14:47] Filtering fusions with no coverage around the breakpoints (remaining=1659)
[2026-06-08T09:14:48] Indexing gene sequences 
[2026-06-08T09:14:55] Filtering genes with >=30% identity (remaining=489)
[2026-06-08T09:14:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=175)
[2026-06-08T09:15:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=161)
[2026-06-08T09:15:01] Searching for additional isoforms (remaining=201)
[2026-06-08T09:15:03] Assigning confidence scores to events 
[2026-06-08T09:15:07] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:15:07] Writing fusions to file 'aih-tih-sc-ea6ef3-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:15:09] Writing discarded fusions to file 'aih-tih-sc-ea6ef3-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:15:41] Freeing resources
[2026-06-08T09:16:02] Done (elapsed time=00:12:51, CPU time=00:12:50, peak memory=17.2gb)