[2026-06-04T21:07:50] Launching Arriba 2.4.0
[2026-06-04T21:07:50] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:08:01] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:08:04] Reading chimeric alignments from '659_cYf-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=14178526)
[2026-06-04T21:14:32] Marking multi-mapping alignments (marked=9265204)
[2026-06-04T21:14:36] Detecting strandedness (no)
[2026-06-04T21:14:36] Annotating alignments 
[2026-06-04T21:15:14] Filtering duplicates (remaining=8271408)
[2026-06-04T21:15:21] 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=7754648)
[2026-06-04T21:15:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7754648)
[2026-06-04T21:15:26] Filtering viral contigs with expression lower than the top 5 (remaining=7754648)
[2026-06-04T21:15:31] Filtering viral contigs with less than 5% coverage (remaining=7754648)
[2026-06-04T21:15:33] Estimating fragment length (mate gap mean=-83.8669, mate gap stddev=27.0224, read length mean=125.442)
[2026-06-04T21:15:34] Filtering read-through fragments with a distance <=10000bp (remaining=7349768)
[2026-06-04T21:15:36] Filtering inconsistently clipped mates (remaining=7174396)
[2026-06-04T21:15:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6935204)
[2026-06-04T21:15:42] Filtering fragments with small insert size (remaining=6933195)
[2026-06-04T21:15:44] Filtering alignments with long gaps (remaining=6933195)
[2026-06-04T21:15:47] Filtering fragments with both mates in the same gene (remaining=6932135)
[2026-06-04T21:15:49] Filtering fusions arising from hairpin structures (remaining=6387301)
[2026-06-04T21:15:51] Filtering reads with a mismatch p-value <=0.01 (remaining=3207699)
[2026-06-04T21:16:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=1294293)
[2026-06-04T21:16:16] Finding fusions and counting supporting reads (total=978657)
[2026-06-04T21:16:31] Merging adjacent fusion breakpoints (remaining=961929)
[2026-06-04T21:16:33] Filtering multi-mapping fusions by alignment score and read support (remaining=542566)
[2026-06-04T21:17:06] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:17:12] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=540009)
[2026-06-04T21:17:13] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=321159)
[2026-06-04T21:17:14] Filtering fusions with <2 supporting reads (remaining=37079)
[2026-06-04T21:17:15] Filtering fusions with an e-value >=0.3 (remaining=8579)
[2026-06-04T21:17:16] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8667)
[2026-06-04T21:17:20] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8447)
[2026-06-04T21:17:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8448)
[2026-06-04T21:17:22] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7033)
[2026-06-04T21:17:28] Searching for fusions with spliced split reads (remaining=7147)
[2026-06-04T21:17:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=4652)
[2026-06-04T21:17:34] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4597)
[2026-06-04T21:17:35] Searching for fusions with >=4 spliced events (remaining=5561)
[2026-06-04T21:17:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2227)
[2026-06-04T21:17:50] Filtering fusions with anchors <=23nt (remaining=1819)
[2026-06-04T21:17:51] Filtering end-to-end fusions with low support (remaining=1768)
[2026-06-04T21:17:52] Filtering fusions with no coverage around the breakpoints (remaining=1721)
[2026-06-04T21:17:52] Indexing gene sequences 
[2026-06-04T21:17:58] Filtering genes with >=30% identity (remaining=584)
[2026-06-04T21:18:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=247)
[2026-06-04T21:18:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=199)
[2026-06-04T21:18:06] Searching for additional isoforms (remaining=273)
[2026-06-04T21:18:07] Assigning confidence scores to events 
[2026-06-04T21:18:11] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:18:11] Writing fusions to file '659_cYf-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:18:16] Writing discarded fusions to file '659_cYf-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:18:43] Freeing resources
[2026-06-04T21:19:02] Done (elapsed time=00:11:12, CPU time=00:11:11, peak memory=18.9gb)