[2026-06-08T08:36:48] Launching Arriba 2.4.0
[2026-06-08T08:36:48] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:37:03] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:37:07] Reading chimeric alignments from '659_bGW-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11085898)
[2026-06-08T08:45:25] Marking multi-mapping alignments (marked=7000356)
[2026-06-08T08:45:30] Detecting strandedness (reverse)
[2026-06-08T08:45:30] Assigning strands to alignments 
[2026-06-08T08:45:33] Annotating alignments 
[2026-06-08T08:46:12] Filtering duplicates (remaining=7605661)
[2026-06-08T08:46:21] 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)
[2026-06-08T08:46:23] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7150718)
[2026-06-08T08:46:25] Filtering viral contigs with expression lower than the top 5 (remaining=7150718)
[2026-06-08T08:46:31] Filtering viral contigs with less than 5% coverage (remaining=7150718)
[2026-06-08T08:46:34] Estimating fragment length (mate gap mean=-83.3903, mate gap stddev=28.7033, read length mean=126.565)
[2026-06-08T08:46:34] Filtering read-through fragments with a distance <=10000bp (remaining=6689704)
[2026-06-08T08:46:36] Filtering inconsistently clipped mates (remaining=6585939)
[2026-06-08T08:46:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6447996)
[2026-06-08T08:46:44] Filtering fragments with small insert size (remaining=6446632)
[2026-06-08T08:46:46] Filtering alignments with long gaps (remaining=6446631)
[2026-06-08T08:46:49] Filtering fragments with both mates in the same gene (remaining=6445457)
[2026-06-08T08:46:51] Filtering fusions arising from hairpin structures (remaining=6106186)
[2026-06-08T08:46:54] Filtering reads with a mismatch p-value <=0.01 (remaining=3222912)
[2026-06-08T08:47:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=1290122)
[2026-06-08T08:47:26] Finding fusions and counting supporting reads (total=913144)
[2026-06-08T08:47:44] Merging adjacent fusion breakpoints (remaining=905975)
[2026-06-08T08:47:46] Filtering multi-mapping fusions by alignment score and read support (remaining=576266)
[2026-06-08T08:48:24] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:48:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=574876)
[2026-06-08T08:48:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=339843)
[2026-06-08T08:48:34] Filtering fusions with <2 supporting reads (remaining=41392)
[2026-06-08T08:48:35] Filtering fusions with an e-value >=0.3 (remaining=10363)
[2026-06-08T08:48:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10436)
[2026-06-08T08:48:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10379)
[2026-06-08T08:48:41] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10379)
[2026-06-08T08:48:43] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7491)
[2026-06-08T08:48:49] Searching for fusions with spliced split reads (remaining=7598)
[2026-06-08T08:48:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=4845)
[2026-06-08T08:48:56] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4793)
[2026-06-08T08:48:57] Searching for fusions with >=4 spliced events (remaining=5761)
[2026-06-08T08:48:59] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2233)
[2026-06-08T08:49:16] Filtering fusions with anchors <=23nt (remaining=1706)
[2026-06-08T08:49:17] Filtering end-to-end fusions with low support (remaining=1687)
[2026-06-08T08:49:18] Filtering fusions with no coverage around the breakpoints (remaining=1656)
[2026-06-08T08:49:18] Indexing gene sequences 
[2026-06-08T08:49:25] Filtering genes with >=30% identity (remaining=548)
[2026-06-08T08:49:28] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=245)
[2026-06-08T08:49:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=214)
[2026-06-08T08:49:37] Searching for additional isoforms (remaining=269)
[2026-06-08T08:49:38] Assigning confidence scores to events 
[2026-06-08T08:49:42] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:49:42] Writing fusions to file '659_bGW-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:49:45] Writing discarded fusions to file '659_bGW-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:20] Freeing resources
[2026-06-08T08:50:39] Done (elapsed time=00:13:51, CPU time=00:13:49, peak memory=15.6gb)