[2026-06-08T08:52:33] Launching Arriba 2.4.0
[2026-06-08T08:52:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:45] Reading chimeric alignments from '659_cfy-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=11173935)
[2026-06-08T09:00:04] Marking multi-mapping alignments (marked=6524229)
[2026-06-08T09:00:09] Detecting strandedness (reverse)
[2026-06-08T09:00:09] Assigning strands to alignments 
[2026-06-08T09:00:12] Annotating alignments 
[2026-06-08T09:00:57] Filtering duplicates (remaining=7082692)
[2026-06-08T09:01:06] 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=6907160)
[2026-06-08T09:01:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6907160)
[2026-06-08T09:01:12] Filtering viral contigs with expression lower than the top 5 (remaining=6907160)
[2026-06-08T09:01:18] Filtering viral contigs with less than 5% coverage (remaining=6907160)
[2026-06-08T09:01:21] Estimating fragment length (mate gap mean=-88.5891, mate gap stddev=29.3019, read length mean=139.613)
[2026-06-08T09:01:21] Filtering read-through fragments with a distance <=10000bp (remaining=6448507)
[2026-06-08T09:01:24] Filtering inconsistently clipped mates (remaining=6365791)
[2026-06-08T09:01:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6191677)
[2026-06-08T09:01:32] Filtering fragments with small insert size (remaining=6191068)
[2026-06-08T09:01:34] Filtering alignments with long gaps (remaining=6191068)
[2026-06-08T09:01:37] Filtering fragments with both mates in the same gene (remaining=6190271)
[2026-06-08T09:01:39] Filtering fusions arising from hairpin structures (remaining=5856156)
[2026-06-08T09:01:43] Filtering reads with a mismatch p-value <=0.01 (remaining=3076037)
[2026-06-08T09:01:58] Filtering reads with low entropy (k-mer content >=60%) (remaining=1076900)
[2026-06-08T09:02:11] Finding fusions and counting supporting reads (total=836597)
[2026-06-08T09:02:32] Merging adjacent fusion breakpoints (remaining=828786)
[2026-06-08T09:02:34] Filtering multi-mapping fusions by alignment score and read support (remaining=560629)
[2026-06-08T09:03:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:03:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=558732)
[2026-06-08T09:03:23] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=284533)
[2026-06-08T09:03:24] Filtering fusions with <2 supporting reads (remaining=42642)
[2026-06-08T09:03:25] Filtering fusions with an e-value >=0.3 (remaining=13803)
[2026-06-08T09:03:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13855)
[2026-06-08T09:03:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13779)
[2026-06-08T09:03:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13867)
[2026-06-08T09:03:33] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8708)
[2026-06-08T09:03:39] Searching for fusions with spliced split reads (remaining=8821)
[2026-06-08T09:03:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=4974)
[2026-06-08T09:03:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4916)
[2026-06-08T09:03:47] Searching for fusions with >=4 spliced events (remaining=6080)
[2026-06-08T09:03:49] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2327)
[2026-06-08T09:04:03] Filtering fusions with anchors <=23nt (remaining=1906)
[2026-06-08T09:04:04] Filtering end-to-end fusions with low support (remaining=1871)
[2026-06-08T09:04:05] Filtering fusions with no coverage around the breakpoints (remaining=1821)
[2026-06-08T09:04:05] Indexing gene sequences 
[2026-06-08T09:04:12] Filtering genes with >=30% identity (remaining=547)
[2026-06-08T09:04:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=215)
[2026-06-08T09:04:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=193)
[2026-06-08T09:04:20] Searching for additional isoforms (remaining=253)
[2026-06-08T09:04:22] Assigning confidence scores to events 
[2026-06-08T09:04:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:04:26] Writing fusions to file '659_cfy-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:04:28] Writing discarded fusions to file '659_cfy-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:05:03] Freeing resources
[2026-06-08T09:05:24] Done (elapsed time=00:12:51, CPU time=00:12:51, peak memory=15.7gb)