[2026-06-04T21:13:55] Launching Arriba 2.4.0
[2026-06-04T21:13:55] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:14:03] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:14:06] Reading chimeric alignments from '659_dfA-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11431466)
[2026-06-04T21:20:56] Marking multi-mapping alignments (marked=6835097)
[2026-06-04T21:21:01] Detecting strandedness (reverse)
[2026-06-04T21:21:01] Assigning strands to alignments 
[2026-06-04T21:21:03] Annotating alignments 
[2026-06-04T21:21:37] Filtering duplicates (remaining=8690436)
[2026-06-04T21:21:45] 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=8286360)
[2026-06-04T21:21:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8286360)
[2026-06-04T21:21:50] Filtering viral contigs with expression lower than the top 5 (remaining=8286360)
[2026-06-04T21:21:56] Filtering viral contigs with less than 5% coverage (remaining=8286360)
[2026-06-04T21:21:58] Estimating fragment length (mate gap mean=-83.3724, mate gap stddev=30.9921, read length mean=135.583)
[2026-06-04T21:21:58] Filtering read-through fragments with a distance <=10000bp (remaining=7807105)
[2026-06-04T21:22:01] Filtering inconsistently clipped mates (remaining=7695784)
[2026-06-04T21:22:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7468865)
[2026-06-04T21:22:08] Filtering fragments with small insert size (remaining=7467960)
[2026-06-04T21:22:11] Filtering alignments with long gaps (remaining=7467960)
[2026-06-04T21:22:13] Filtering fragments with both mates in the same gene (remaining=7466262)
[2026-06-04T21:22:16] Filtering fusions arising from hairpin structures (remaining=7041156)
[2026-06-04T21:22:19] Filtering reads with a mismatch p-value <=0.01 (remaining=4008723)
[2026-06-04T21:22:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=1735571)
[2026-06-04T21:22:51] Finding fusions and counting supporting reads (total=1327947)
[2026-06-04T21:23:10] Merging adjacent fusion breakpoints (remaining=1321028)
[2026-06-04T21:23:12] Filtering multi-mapping fusions by alignment score and read support (remaining=846773)
[2026-06-04T21:23:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:23:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=841904)
[2026-06-04T21:23:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=552057)
[2026-06-04T21:23:58] Filtering fusions with <2 supporting reads (remaining=55242)
[2026-06-04T21:23:59] Filtering fusions with an e-value >=0.3 (remaining=17028)
[2026-06-04T21:24:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=17088)
[2026-06-04T21:24:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=16988)
[2026-06-04T21:24:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=17039)
[2026-06-04T21:24:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10806)
[2026-06-04T21:24:14] Searching for fusions with spliced split reads (remaining=10946)
[2026-06-04T21:24:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=5069)
[2026-06-04T21:24:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5008)
[2026-06-04T21:24:23] Searching for fusions with >=4 spliced events (remaining=6593)
[2026-06-04T21:24:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2698)
[2026-06-04T21:24:38] Filtering fusions with anchors <=23nt (remaining=2221)
[2026-06-04T21:24:39] Filtering end-to-end fusions with low support (remaining=2188)
[2026-06-04T21:24:40] Filtering fusions with no coverage around the breakpoints (remaining=2154)
[2026-06-04T21:24:41] Indexing gene sequences 
[2026-06-04T21:24:49] Filtering genes with >=30% identity (remaining=709)
[2026-06-04T21:25:02] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=405)
[2026-06-04T21:25:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=271)
[2026-06-04T21:25:34] Searching for additional isoforms (remaining=399)
[2026-06-04T21:25:36] Assigning confidence scores to events 
[2026-06-04T21:25:41] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:25:41] Writing fusions to file '659_dfA-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:25:46] Writing discarded fusions to file '659_dfA-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:26:20] Freeing resources
[2026-06-04T21:26:41] Done (elapsed time=00:12:46, CPU time=00:12:45, peak memory=16.3gb)