[2026-06-04T21:18:37] Launching Arriba 2.4.0
[2026-06-04T21:18:37] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:18:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:18:49] Reading chimeric alignments from '659_cB6-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=14651034)
[2026-06-04T21:25:55] Marking multi-mapping alignments (marked=10131114)
[2026-06-04T21:26:00] Detecting strandedness (reverse)
[2026-06-04T21:26:00] Assigning strands to alignments 
[2026-06-04T21:26:03] Annotating alignments 
[2026-06-04T21:26:45] Filtering duplicates (remaining=3363195)
[2026-06-04T21:26:52] 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=2970279)
[2026-06-04T21:26:54] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2970279)
[2026-06-04T21:26:57] Filtering viral contigs with expression lower than the top 5 (remaining=2970279)
[2026-06-04T21:27:03] Filtering viral contigs with less than 5% coverage (remaining=2970279)
[2026-06-04T21:27:06] Estimating fragment length (mate gap mean=-83.1986, mate gap stddev=30.824, read length mean=133.899)
[2026-06-04T21:27:06] Filtering read-through fragments with a distance <=10000bp (remaining=2882803)
[2026-06-04T21:27:09] Filtering inconsistently clipped mates (remaining=2845391)
[2026-06-04T21:27:12] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2713926)
[2026-06-04T21:27:16] Filtering fragments with small insert size (remaining=2713506)
[2026-06-04T21:27:19] Filtering alignments with long gaps (remaining=2713506)
[2026-06-04T21:27:21] Filtering fragments with both mates in the same gene (remaining=2712946)
[2026-06-04T21:27:24] Filtering fusions arising from hairpin structures (remaining=2592354)
[2026-06-04T21:27:27] Filtering reads with a mismatch p-value <=0.01 (remaining=1130713)
[2026-06-04T21:27:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=257005)
[2026-06-04T21:27:44] Finding fusions and counting supporting reads (total=184971)
[2026-06-04T21:27:59] Merging adjacent fusion breakpoints (remaining=183948)
[2026-06-04T21:28:00] Filtering multi-mapping fusions by alignment score and read support (remaining=107492)
[2026-06-04T21:28:38] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:28:41] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=105676)
[2026-06-04T21:28:42] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=64162)
[2026-06-04T21:28:42] Filtering fusions with <2 supporting reads (remaining=6748)
[2026-06-04T21:28:43] Filtering fusions with an e-value >=0.3 (remaining=2491)
[2026-06-04T21:28:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2509)
[2026-06-04T21:28:47] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2431)
[2026-06-04T21:28:47] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2431)
[2026-06-04T21:28:48] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1803)
[2026-06-04T21:28:52] Searching for fusions with spliced split reads (remaining=1877)
[2026-06-04T21:28:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=1277)
[2026-06-04T21:28:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1235)
[2026-06-04T21:28:58] Searching for fusions with >=4 spliced events (remaining=1353)
[2026-06-04T21:28:59] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=448)
[2026-06-04T21:29:10] Filtering fusions with anchors <=23nt (remaining=365)
[2026-06-04T21:29:11] Filtering end-to-end fusions with low support (remaining=350)
[2026-06-04T21:29:11] Filtering fusions with no coverage around the breakpoints (remaining=337)
[2026-06-04T21:29:11] Indexing gene sequences 
[2026-06-04T21:29:14] Filtering genes with >=30% identity (remaining=175)
[2026-06-04T21:29:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=119)
[2026-06-04T21:29:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=110)
[2026-06-04T21:29:18] Searching for additional isoforms (remaining=125)
[2026-06-04T21:29:18] Assigning confidence scores to events 
[2026-06-04T21:29:20] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:29:20] Writing fusions to file '659_cB6-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:29:21] Writing discarded fusions to file '659_cB6-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:29:34] Freeing resources
[2026-06-04T21:29:56] Done (elapsed time=00:11:19, CPU time=00:11:18, peak memory=18.8gb)