[2026-06-04T21:19:21] Launching Arriba 2.4.0
[2026-06-04T21:19:21] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:19:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:19:33] Reading chimeric alignments from '659_b7Z-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=9916912)
[2026-06-04T21:26:26] Marking multi-mapping alignments (marked=6070450)
[2026-06-04T21:26:30] Detecting strandedness (reverse)
[2026-06-04T21:26:30] Assigning strands to alignments 
[2026-06-04T21:26:32] Annotating alignments 
[2026-06-04T21:27:02] Filtering duplicates (remaining=6967486)
[2026-06-04T21:27:10] 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=6715797)
[2026-06-04T21:27:12] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6715797)
[2026-06-04T21:27:14] Filtering viral contigs with expression lower than the top 5 (remaining=6715797)
[2026-06-04T21:27:18] Filtering viral contigs with less than 5% coverage (remaining=6715797)
[2026-06-04T21:27:21] Estimating fragment length (mate gap mean=-87.1979, mate gap stddev=30.5285, read length mean=136.746)
[2026-06-04T21:27:21] Filtering read-through fragments with a distance <=10000bp (remaining=6161449)
[2026-06-04T21:27:23] Filtering inconsistently clipped mates (remaining=6072591)
[2026-06-04T21:27:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5827396)
[2026-06-04T21:27:29] Filtering fragments with small insert size (remaining=5826787)
[2026-06-04T21:27:31] Filtering alignments with long gaps (remaining=5826785)
[2026-06-04T21:27:33] Filtering fragments with both mates in the same gene (remaining=5825680)
[2026-06-04T21:27:35] Filtering fusions arising from hairpin structures (remaining=5483931)
[2026-06-04T21:27:38] Filtering reads with a mismatch p-value <=0.01 (remaining=2915172)
[2026-06-04T21:27:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=1315001)
[2026-06-04T21:28:02] Finding fusions and counting supporting reads (total=940800)
[2026-06-04T21:28:18] Merging adjacent fusion breakpoints (remaining=929409)
[2026-06-04T21:28:20] Filtering multi-mapping fusions by alignment score and read support (remaining=590831)
[2026-06-04T21:28:50] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:28:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=587371)
[2026-06-04T21:28:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=300212)
[2026-06-04T21:29:00] Filtering fusions with <2 supporting reads (remaining=48998)
[2026-06-04T21:29:01] Filtering fusions with an e-value >=0.3 (remaining=17994)
[2026-06-04T21:29:01] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=18048)
[2026-06-04T21:29:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=17916)
[2026-06-04T21:29:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=17916)
[2026-06-04T21:29:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=11234)
[2026-06-04T21:29:13] Searching for fusions with spliced split reads (remaining=11305)
[2026-06-04T21:29:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=5737)
[2026-06-04T21:29:19] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5676)
[2026-06-04T21:29:20] Searching for fusions with >=4 spliced events (remaining=6880)
[2026-06-04T21:29:21] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2569)
[2026-06-04T21:29:41] Filtering fusions with anchors <=23nt (remaining=1972)
[2026-06-04T21:29:41] Filtering end-to-end fusions with low support (remaining=1926)
[2026-06-04T21:29:42] Filtering fusions with no coverage around the breakpoints (remaining=1877)
[2026-06-04T21:29:43] Indexing gene sequences 
[2026-06-04T21:29:49] Filtering genes with >=30% identity (remaining=570)
[2026-06-04T21:29:52] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=251)
[2026-06-04T21:30:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=199)
[2026-06-04T21:30:03] Searching for additional isoforms (remaining=264)
[2026-06-04T21:30:04] Assigning confidence scores to events 
[2026-06-04T21:30:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:30:08] Writing fusions to file '659_b7Z-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:30:10] Writing discarded fusions to file '659_b7Z-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:30:38] Freeing resources
[2026-06-04T21:30:56] Done (elapsed time=00:11:35, CPU time=00:11:34, peak memory=14.7gb)