[2026-06-08T08:52:30] Launching Arriba 2.4.0
[2026-06-08T08:52:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:44] Reading chimeric alignments from '659_cWx-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=12458172)
[2026-06-08T09:00:36] Marking multi-mapping alignments (marked=7820392)
[2026-06-08T09:00:42] Detecting strandedness (reverse)
[2026-06-08T09:00:42] Assigning strands to alignments 
[2026-06-08T09:00:45] Annotating alignments 
[2026-06-08T09:01:37] Filtering duplicates (remaining=5623247)
[2026-06-08T09:01:47] 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=5364060)
[2026-06-08T09:01:50] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5364060)
[2026-06-08T09:01:53] Filtering viral contigs with expression lower than the top 5 (remaining=5364060)
[2026-06-08T09:02:00] Filtering viral contigs with less than 5% coverage (remaining=5364060)
[2026-06-08T09:02:04] Estimating fragment length (mate gap mean=-89.7207, mate gap stddev=29.6547, read length mean=140.054)
[2026-06-08T09:02:04] Filtering read-through fragments with a distance <=10000bp (remaining=5063185)
[2026-06-08T09:02:07] Filtering inconsistently clipped mates (remaining=4997598)
[2026-06-08T09:02:11] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4791534)
[2026-06-08T09:02:17] Filtering fragments with small insert size (remaining=4791020)
[2026-06-08T09:02:21] Filtering alignments with long gaps (remaining=4791017)
[2026-06-08T09:02:25] Filtering fragments with both mates in the same gene (remaining=4790372)
[2026-06-08T09:02:29] Filtering fusions arising from hairpin structures (remaining=4581575)
[2026-06-08T09:02:33] Filtering reads with a mismatch p-value <=0.01 (remaining=2193301)
[2026-06-08T09:02:57] Filtering reads with low entropy (k-mer content >=60%) (remaining=617841)
[2026-06-08T09:03:11] Finding fusions and counting supporting reads (total=510349)
[2026-06-08T09:03:38] Merging adjacent fusion breakpoints (remaining=506590)
[2026-06-08T09:03:40] Filtering multi-mapping fusions by alignment score and read support (remaining=303496)
[2026-06-08T09:04:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:04:37] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=299939)
[2026-06-08T09:04:38] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=168776)
[2026-06-08T09:04:39] Filtering fusions with <2 supporting reads (remaining=21118)
[2026-06-08T09:04:40] Filtering fusions with an e-value >=0.3 (remaining=7143)
[2026-06-08T09:04:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7195)
[2026-06-08T09:04:45] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7084)
[2026-06-08T09:04:46] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7085)
[2026-06-08T09:04:47] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5394)
[2026-06-08T09:04:53] Searching for fusions with spliced split reads (remaining=5476)
[2026-06-08T09:05:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=3322)
[2026-06-08T09:05:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3275)
[2026-06-08T09:05:02] Searching for fusions with >=4 spliced events (remaining=3695)
[2026-06-08T09:05:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1235)
[2026-06-08T09:05:21] Filtering fusions with anchors <=23nt (remaining=895)
[2026-06-08T09:05:22] Filtering end-to-end fusions with low support (remaining=851)
[2026-06-08T09:05:23] Filtering fusions with no coverage around the breakpoints (remaining=810)
[2026-06-08T09:05:23] Indexing gene sequences 
[2026-06-08T09:05:29] Filtering genes with >=30% identity (remaining=273)
[2026-06-08T09:05:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=110)
[2026-06-08T09:05:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=107)
[2026-06-08T09:05:34] Searching for additional isoforms (remaining=149)
[2026-06-08T09:05:35] Assigning confidence scores to events 
[2026-06-08T09:05:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:05:39] Writing fusions to file '659_cWx-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T09:05:40] Writing discarded fusions to file '659_cWx-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:06:11] Freeing resources
[2026-06-08T09:06:41] Done (elapsed time=00:14:11, CPU time=00:14:10, peak memory=16.7gb)