[2026-06-08T08:54:31] Launching Arriba 2.4.0
[2026-06-08T08:54:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:54:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:54:43] Reading chimeric alignments from '659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=12056969)
[2026-06-08T09:02:09] Marking multi-mapping alignments (marked=7304943)
[2026-06-08T09:02:15] Detecting strandedness (reverse)
[2026-06-08T09:02:15] Assigning strands to alignments 
[2026-06-08T09:02:18] Annotating alignments 
[2026-06-08T09:03:06] Filtering duplicates (remaining=6373013)
[2026-06-08T09:03:15] 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=6174701)
[2026-06-08T09:03:18] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6174701)
[2026-06-08T09:03:21] Filtering viral contigs with expression lower than the top 5 (remaining=6174701)
[2026-06-08T09:03:28] Filtering viral contigs with less than 5% coverage (remaining=6174701)
[2026-06-08T09:03:31] Estimating fragment length (mate gap mean=-91.0127, mate gap stddev=28.0845, read length mean=134.746)
[2026-06-08T09:03:32] Filtering read-through fragments with a distance <=10000bp (remaining=5818277)
[2026-06-08T09:03:35] Filtering inconsistently clipped mates (remaining=5723419)
[2026-06-08T09:03:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5537249)
[2026-06-08T09:03:44] Filtering fragments with small insert size (remaining=5536507)
[2026-06-08T09:03:46] Filtering alignments with long gaps (remaining=5536507)
[2026-06-08T09:03:49] Filtering fragments with both mates in the same gene (remaining=5535634)
[2026-06-08T09:03:52] Filtering fusions arising from hairpin structures (remaining=5215024)
[2026-06-08T09:03:56] Filtering reads with a mismatch p-value <=0.01 (remaining=2563142)
[2026-06-08T09:04:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=930954)
[2026-06-08T09:04:24] Finding fusions and counting supporting reads (total=749465)
[2026-06-08T09:04:43] Merging adjacent fusion breakpoints (remaining=742761)
[2026-06-08T09:04:45] Filtering multi-mapping fusions by alignment score and read support (remaining=471463)
[2026-06-08T09:05:28] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:05:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=469459)
[2026-06-08T09:05:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=249449)
[2026-06-08T09:05:38] Filtering fusions with <2 supporting reads (remaining=29192)
[2026-06-08T09:05:38] Filtering fusions with an e-value >=0.3 (remaining=7103)
[2026-06-08T09:05:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7163)
[2026-06-08T09:05:44] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7037)
[2026-06-08T09:05:44] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7040)
[2026-06-08T09:05:46] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6391)
[2026-06-08T09:05:52] Searching for fusions with spliced split reads (remaining=6508)
[2026-06-08T09:05:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=4325)
[2026-06-08T09:05:59] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4281)
[2026-06-08T09:06:00] Searching for fusions with >=4 spliced events (remaining=5063)
[2026-06-08T09:06:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1662)
[2026-06-08T09:06:15] Filtering fusions with anchors <=23nt (remaining=1363)
[2026-06-08T09:06:16] Filtering end-to-end fusions with low support (remaining=1322)
[2026-06-08T09:06:17] Filtering fusions with no coverage around the breakpoints (remaining=1290)
[2026-06-08T09:06:18] Indexing gene sequences 
[2026-06-08T09:06:24] Filtering genes with >=30% identity (remaining=415)
[2026-06-08T09:06:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=181)
[2026-06-08T09:06:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=174)
[2026-06-08T09:06:32] Searching for additional isoforms (remaining=209)
[2026-06-08T09:06:34] Assigning confidence scores to events 
[2026-06-08T09:06:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:06:38] Writing fusions to file '659_bGc-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:06:40] Writing discarded fusions to file '659_bGc-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:07:11] Freeing resources
[2026-06-08T09:07:31] Done (elapsed time=00:13:00, CPU time=00:12:59, peak memory=16.6gb)