[2026-06-04T21:15:46] Launching Arriba 2.4.0
[2026-06-04T21:15:46] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:15:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:15:57] Reading chimeric alignments from '659_c95-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11378551)
[2026-06-04T21:22:43] Marking multi-mapping alignments (marked=7077043)
[2026-06-04T21:22:47] Detecting strandedness (reverse)
[2026-06-04T21:22:47] Assigning strands to alignments 
[2026-06-04T21:22:50] Annotating alignments 
[2026-06-04T21:23:24] Filtering duplicates (remaining=8188673)
[2026-06-04T21:23:32] 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=7779835)
[2026-06-04T21:23:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7779835)
[2026-06-04T21:23:36] Filtering viral contigs with expression lower than the top 5 (remaining=7779835)
[2026-06-04T21:23:42] Filtering viral contigs with less than 5% coverage (remaining=7779835)
[2026-06-04T21:23:44] Estimating fragment length (mate gap mean=-86.2452, mate gap stddev=29.4214, read length mean=132.501)
[2026-06-04T21:23:44] Filtering read-through fragments with a distance <=10000bp (remaining=7302671)
[2026-06-04T21:23:47] Filtering inconsistently clipped mates (remaining=7181098)
[2026-06-04T21:23:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6976192)
[2026-06-04T21:23:54] Filtering fragments with small insert size (remaining=6975102)
[2026-06-04T21:23:56] Filtering alignments with long gaps (remaining=6975102)
[2026-06-04T21:23:58] Filtering fragments with both mates in the same gene (remaining=6973895)
[2026-06-04T21:24:01] Filtering fusions arising from hairpin structures (remaining=6525702)
[2026-06-04T21:24:04] Filtering reads with a mismatch p-value <=0.01 (remaining=3539660)
[2026-06-04T21:24:20] Filtering reads with low entropy (k-mer content >=60%) (remaining=1547872)
[2026-06-04T21:24:33] Finding fusions and counting supporting reads (total=1143131)
[2026-06-04T21:24:51] Merging adjacent fusion breakpoints (remaining=1132509)
[2026-06-04T21:24:54] Filtering multi-mapping fusions by alignment score and read support (remaining=696959)
[2026-06-04T21:25:28] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:25:37] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=693956)
[2026-06-04T21:25:38] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=425694)
[2026-06-04T21:25:39] Filtering fusions with <2 supporting reads (remaining=48495)
[2026-06-04T21:25:40] Filtering fusions with an e-value >=0.3 (remaining=13747)
[2026-06-04T21:25:41] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13838)
[2026-06-04T21:25:46] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13700)
[2026-06-04T21:25:47] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13702)
[2026-06-04T21:25:49] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9432)
[2026-06-04T21:25:55] Searching for fusions with spliced split reads (remaining=9502)
[2026-06-04T21:26:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=5332)
[2026-06-04T21:26:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5247)
[2026-06-04T21:26:04] Searching for fusions with >=4 spliced events (remaining=6558)
[2026-06-04T21:26:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2695)
[2026-06-04T21:26:26] Filtering fusions with anchors <=23nt (remaining=2066)
[2026-06-04T21:26:27] Filtering end-to-end fusions with low support (remaining=2018)
[2026-06-04T21:26:28] Filtering fusions with no coverage around the breakpoints (remaining=1965)
[2026-06-04T21:26:29] Indexing gene sequences 
[2026-06-04T21:26:35] Filtering genes with >=30% identity (remaining=659)
[2026-06-04T21:26:39] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=343)
[2026-06-04T21:26:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=256)
[2026-06-04T21:26:50] Searching for additional isoforms (remaining=413)
[2026-06-04T21:26:52] Assigning confidence scores to events 
[2026-06-04T21:26:56] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:26:56] Writing fusions to file '659_c95-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:27:00] Writing discarded fusions to file '659_c95-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:27:34] Freeing resources
[2026-06-04T21:27:54] Done (elapsed time=00:12:08, CPU time=00:12:07, peak memory=16.2gb)