[2026-06-04T21:14:47] Launching Arriba 2.4.0
[2026-06-04T21:14:47] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:14:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:14:58] Reading chimeric alignments from '659_bGW-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11085898)
[2026-06-04T21:21:27] Marking multi-mapping alignments (marked=7000356)
[2026-06-04T21:21:31] Detecting strandedness (reverse)
[2026-06-04T21:21:31] Assigning strands to alignments 
[2026-06-04T21:21:33] Annotating alignments 
[2026-06-04T21:22:03] Filtering duplicates (remaining=7605661)
[2026-06-04T21:22:11] 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=7150718)
[2026-06-04T21:22:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7150718)
[2026-06-04T21:22:15] Filtering viral contigs with expression lower than the top 5 (remaining=7150718)
[2026-06-04T21:22:20] Filtering viral contigs with less than 5% coverage (remaining=7150718)
[2026-06-04T21:22:22] Estimating fragment length (mate gap mean=-83.3903, mate gap stddev=28.7033, read length mean=126.565)
[2026-06-04T21:22:22] Filtering read-through fragments with a distance <=10000bp (remaining=6689704)
[2026-06-04T21:22:25] Filtering inconsistently clipped mates (remaining=6585939)
[2026-06-04T21:22:27] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6447996)
[2026-06-04T21:22:31] Filtering fragments with small insert size (remaining=6446632)
[2026-06-04T21:22:33] Filtering alignments with long gaps (remaining=6446631)
[2026-06-04T21:22:35] Filtering fragments with both mates in the same gene (remaining=6445457)
[2026-06-04T21:22:38] Filtering fusions arising from hairpin structures (remaining=6106186)
[2026-06-04T21:22:40] Filtering reads with a mismatch p-value <=0.01 (remaining=3222912)
[2026-06-04T21:22:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=1290122)
[2026-06-04T21:23:05] Finding fusions and counting supporting reads (total=913144)
[2026-06-04T21:23:21] Merging adjacent fusion breakpoints (remaining=905975)
[2026-06-04T21:23:22] Filtering multi-mapping fusions by alignment score and read support (remaining=576266)
[2026-06-04T21:23:53] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:24:00] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=574876)
[2026-06-04T21:24:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=339843)
[2026-06-04T21:24:03] Filtering fusions with <2 supporting reads (remaining=41392)
[2026-06-04T21:24:03] Filtering fusions with an e-value >=0.3 (remaining=10363)
[2026-06-04T21:24:04] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10436)
[2026-06-04T21:24:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10379)
[2026-06-04T21:24:09] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10379)
[2026-06-04T21:24:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7491)
[2026-06-04T21:24:16] Searching for fusions with spliced split reads (remaining=7598)
[2026-06-04T21:24:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=4845)
[2026-06-04T21:24:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4793)
[2026-06-04T21:24:24] Searching for fusions with >=4 spliced events (remaining=5761)
[2026-06-04T21:24:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2233)
[2026-06-04T21:24:39] Filtering fusions with anchors <=23nt (remaining=1706)
[2026-06-04T21:24:40] Filtering end-to-end fusions with low support (remaining=1687)
[2026-06-04T21:24:40] Filtering fusions with no coverage around the breakpoints (remaining=1656)
[2026-06-04T21:24:41] Indexing gene sequences 
[2026-06-04T21:24:47] Filtering genes with >=30% identity (remaining=548)
[2026-06-04T21:24:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=245)
[2026-06-04T21:24:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=214)
[2026-06-04T21:24:57] Searching for additional isoforms (remaining=269)
[2026-06-04T21:24:59] Assigning confidence scores to events 
[2026-06-04T21:25:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:25:02] Writing fusions to file '659_bGW-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:25:04] Writing discarded fusions to file '659_bGW-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:25:33] Freeing resources
[2026-06-04T21:25:50] Done (elapsed time=00:11:03, CPU time=00:11:03, peak memory=15.6gb)