[2026-06-08T08:33:50] Launching Arriba 2.4.0
[2026-06-08T08:33:50] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:33:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:34:03] Reading chimeric alignments from '659_c95-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11378551)
[2026-06-08T08:41:14] Marking multi-mapping alignments (marked=7077043)
[2026-06-08T08:41:19] Detecting strandedness (reverse)
[2026-06-08T08:41:19] Assigning strands to alignments 
[2026-06-08T08:41:22] Annotating alignments 
[2026-06-08T08:42:00] Filtering duplicates (remaining=8188673)
[2026-06-08T08:42:09] 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)
[2026-06-08T08:42:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7779835)
[2026-06-08T08:42:13] Filtering viral contigs with expression lower than the top 5 (remaining=7779835)
[2026-06-08T08:42:18] Filtering viral contigs with less than 5% coverage (remaining=7779835)
[2026-06-08T08:42:21] Estimating fragment length (mate gap mean=-86.2452, mate gap stddev=29.4214, read length mean=132.501)
[2026-06-08T08:42:21] Filtering read-through fragments with a distance <=10000bp (remaining=7302671)
[2026-06-08T08:42:23] Filtering inconsistently clipped mates (remaining=7181098)
[2026-06-08T08:42:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6976192)
[2026-06-08T08:42:31] Filtering fragments with small insert size (remaining=6975102)
[2026-06-08T08:42:33] Filtering alignments with long gaps (remaining=6975102)
[2026-06-08T08:42:36] Filtering fragments with both mates in the same gene (remaining=6973895)
[2026-06-08T08:42:38] Filtering fusions arising from hairpin structures (remaining=6525702)
[2026-06-08T08:42:41] Filtering reads with a mismatch p-value <=0.01 (remaining=3539660)
[2026-06-08T08:42:59] Filtering reads with low entropy (k-mer content >=60%) (remaining=1547872)
[2026-06-08T08:43:13] Finding fusions and counting supporting reads (total=1143131)
[2026-06-08T08:43:36] Merging adjacent fusion breakpoints (remaining=1132509)
[2026-06-08T08:43:38] Filtering multi-mapping fusions by alignment score and read support (remaining=696959)
[2026-06-08T08:44:16] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:44:27] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=693956)
[2026-06-08T08:44:28] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=425694)
[2026-06-08T08:44:29] Filtering fusions with <2 supporting reads (remaining=48495)
[2026-06-08T08:44:30] Filtering fusions with an e-value >=0.3 (remaining=13747)
[2026-06-08T08:44:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13838)
[2026-06-08T08:44:36] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13700)
[2026-06-08T08:44:37] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13702)
[2026-06-08T08:44:39] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9432)
[2026-06-08T08:44:46] Searching for fusions with spliced split reads (remaining=9502)
[2026-06-08T08:44:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=5332)
[2026-06-08T08:44:54] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5247)
[2026-06-08T08:44:55] Searching for fusions with >=4 spliced events (remaining=6558)
[2026-06-08T08:44:57] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2695)
[2026-06-08T08:45:18] Filtering fusions with anchors <=23nt (remaining=2066)
[2026-06-08T08:45:19] Filtering end-to-end fusions with low support (remaining=2018)
[2026-06-08T08:45:20] Filtering fusions with no coverage around the breakpoints (remaining=1965)
[2026-06-08T08:45:21] Indexing gene sequences 
[2026-06-08T08:45:27] Filtering genes with >=30% identity (remaining=659)
[2026-06-08T08:45:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=343)
[2026-06-08T08:45:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=256)
[2026-06-08T08:45:43] Searching for additional isoforms (remaining=413)
[2026-06-08T08:45:44] Assigning confidence scores to events 
[2026-06-08T08:45:49] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:45:49] Writing fusions to file '659_c95-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:45:53] Writing discarded fusions to file '659_c95-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:46:32] Freeing resources
[2026-06-08T08:46:52] Done (elapsed time=00:13:02, CPU time=00:13:01, peak memory=16.1gb)