[2026-06-08T08:54:36] Launching Arriba 2.4.0
[2026-06-08T08:54:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:54:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:54:49] Reading chimeric alignments from '659_ciJ-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=11992447)
[2026-06-08T09:01:55] Marking multi-mapping alignments (marked=7274777)
[2026-06-08T09:01:59] Detecting strandedness (reverse)
[2026-06-08T09:01:59] Assigning strands to alignments 
[2026-06-08T09:02:02] Annotating alignments 
[2026-06-08T09:02:41] Filtering duplicates (remaining=7723523)
[2026-06-08T09:02:50] 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=7496881)
[2026-06-08T09:02:52] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7496881)
[2026-06-08T09:02:55] Filtering viral contigs with expression lower than the top 5 (remaining=7496881)
[2026-06-08T09:03:00] Filtering viral contigs with less than 5% coverage (remaining=7496881)
[2026-06-08T09:03:03] Estimating fragment length (mate gap mean=-88.6036, mate gap stddev=30.5418, read length mean=139.207)
[2026-06-08T09:03:03] Filtering read-through fragments with a distance <=10000bp (remaining=7027443)
[2026-06-08T09:03:05] Filtering inconsistently clipped mates (remaining=6933665)
[2026-06-08T09:03:07] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6672087)
[2026-06-08T09:03:12] Filtering fragments with small insert size (remaining=6671367)
[2026-06-08T09:03:15] Filtering alignments with long gaps (remaining=6671367)
[2026-06-08T09:03:17] Filtering fragments with both mates in the same gene (remaining=6670233)
[2026-06-08T09:03:20] Filtering fusions arising from hairpin structures (remaining=6296388)
[2026-06-08T09:03:22] Filtering reads with a mismatch p-value <=0.01 (remaining=3304581)
[2026-06-08T09:03:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=1187885)
[2026-06-08T09:03:52] Finding fusions and counting supporting reads (total=944963)
[2026-06-08T09:04:12] Merging adjacent fusion breakpoints (remaining=937228)
[2026-06-08T09:04:14] Filtering multi-mapping fusions by alignment score and read support (remaining=601478)
[2026-06-08T09:04:53] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:05:03] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=598119)
[2026-06-08T09:05:04] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=330433)
[2026-06-08T09:05:05] Filtering fusions with <2 supporting reads (remaining=43912)
[2026-06-08T09:05:06] Filtering fusions with an e-value >=0.3 (remaining=15591)
[2026-06-08T09:05:07] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=15657)
[2026-06-08T09:05:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=15517)
[2026-06-08T09:05:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=15523)
[2026-06-08T09:05:15] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9713)
[2026-06-08T09:05:21] Searching for fusions with spliced split reads (remaining=9741)
[2026-06-08T09:05:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=5215)
[2026-06-08T09:05:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5151)
[2026-06-08T09:05:30] Searching for fusions with >=4 spliced events (remaining=6211)
[2026-06-08T09:05:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2279)
[2026-06-08T09:05:50] Filtering fusions with anchors <=23nt (remaining=1733)
[2026-06-08T09:05:50] Filtering end-to-end fusions with low support (remaining=1671)
[2026-06-08T09:05:51] Filtering fusions with no coverage around the breakpoints (remaining=1625)
[2026-06-08T09:05:52] Indexing gene sequences 
[2026-06-08T09:05:58] Filtering genes with >=30% identity (remaining=475)
[2026-06-08T09:06:02] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=248)
[2026-06-08T09:06:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=202)
[2026-06-08T09:06:12] Searching for additional isoforms (remaining=255)
[2026-06-08T09:06:13] Assigning confidence scores to events 
[2026-06-08T09:06:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:06:18] Writing fusions to file '659_ciJ-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:06:20] Writing discarded fusions to file '659_ciJ-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:06:57] Freeing resources
[2026-06-08T09:07:17] Done (elapsed time=00:12:41, CPU time=00:12:41, peak memory=16.7gb)