[2026-06-04T21:09:47] Launching Arriba 2.4.0
[2026-06-04T21:09:47] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:09:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:09:59] Reading chimeric alignments from '659_d01-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11304500)
[2026-06-04T21:16:27] Marking multi-mapping alignments (marked=7246949)
[2026-06-04T21:16:31] Detecting strandedness (no)
[2026-06-04T21:16:31] Annotating alignments 
[2026-06-04T21:17:10] Filtering duplicates (remaining=7694091)
[2026-06-04T21:17:18] 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=7245653)
[2026-06-04T21:17:20] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7245653)
[2026-06-04T21:17:22] Filtering viral contigs with expression lower than the top 5 (remaining=7245653)
[2026-06-04T21:17:28] Filtering viral contigs with less than 5% coverage (remaining=7245653)
[2026-06-04T21:17:30] Estimating fragment length (mate gap mean=-84.4075, mate gap stddev=28.9329, read length mean=126.567)
[2026-06-04T21:17:30] Filtering read-through fragments with a distance <=10000bp (remaining=6922981)
[2026-06-04T21:17:33] Filtering inconsistently clipped mates (remaining=6799522)
[2026-06-04T21:17:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6617214)
[2026-06-04T21:17:39] Filtering fragments with small insert size (remaining=6616040)
[2026-06-04T21:17:42] Filtering alignments with long gaps (remaining=6616032)
[2026-06-04T21:17:44] Filtering fragments with both mates in the same gene (remaining=6614876)
[2026-06-04T21:17:46] Filtering fusions arising from hairpin structures (remaining=6214849)
[2026-06-04T21:17:49] Filtering reads with a mismatch p-value <=0.01 (remaining=3166175)
[2026-06-04T21:18:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=1144358)
[2026-06-04T21:18:15] Finding fusions and counting supporting reads (total=878360)
[2026-06-04T21:18:31] Merging adjacent fusion breakpoints (remaining=869968)
[2026-06-04T21:18:33] Filtering multi-mapping fusions by alignment score and read support (remaining=533653)
[2026-06-04T21:19:07] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:19:15] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=531761)
[2026-06-04T21:19:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=332247)
[2026-06-04T21:19:17] Filtering fusions with <2 supporting reads (remaining=31656)
[2026-06-04T21:19:18] Filtering fusions with an e-value >=0.3 (remaining=7096)
[2026-06-04T21:19:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7158)
[2026-06-04T21:19:23] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7010)
[2026-06-04T21:19:24] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7012)
[2026-06-04T21:19:25] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6599)
[2026-06-04T21:19:31] Searching for fusions with spliced split reads (remaining=6620)
[2026-06-04T21:19:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=4461)
[2026-06-04T21:19:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4393)
[2026-06-04T21:19:39] Searching for fusions with >=4 spliced events (remaining=5304)
[2026-06-04T21:19:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2078)
[2026-06-04T21:19:56] Filtering fusions with anchors <=23nt (remaining=1564)
[2026-06-04T21:19:56] Filtering end-to-end fusions with low support (remaining=1516)
[2026-06-04T21:19:57] Filtering fusions with no coverage around the breakpoints (remaining=1474)
[2026-06-04T21:19:58] Indexing gene sequences 
[2026-06-04T21:20:04] Filtering genes with >=30% identity (remaining=461)
[2026-06-04T21:20:08] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=219)
[2026-06-04T21:20:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=191)
[2026-06-04T21:20:13] Searching for additional isoforms (remaining=252)
[2026-06-04T21:20:15] Assigning confidence scores to events 
[2026-06-04T21:20:19] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:20:19] Writing fusions to file '659_d01-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:20:22] Writing discarded fusions to file '659_d01-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:20:52] Freeing resources
[2026-06-04T21:21:10] Done (elapsed time=00:11:23, CPU time=00:11:22, peak memory=15.9gb)