[2026-05-28T00:03:50] Launching Arriba 2.4.0
[2026-05-28T00:03:50] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:03:58] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:04:02] Reading chimeric alignments from '659_djb-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3450912)
[2026-05-28T00:06:14] Marking multi-mapping alignments (marked=2174501)
[2026-05-28T00:06:16] Detecting strandedness (reverse)
[2026-05-28T00:06:16] Assigning strands to alignments 
[2026-05-28T00:06:16] Annotating alignments 
[2026-05-28T00:06:29] Filtering duplicates (remaining=1831803)
[2026-05-28T00:06:31] 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=1744881)
[2026-05-28T00:06:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1744881)
[2026-05-28T00:06:32] Filtering viral contigs with expression lower than the top 5 (remaining=1744881)
[2026-05-28T00:06:34] Filtering viral contigs with less than 5% coverage (remaining=1744881)
[2026-05-28T00:06:35] Estimating fragment length (mate gap mean=-89.3053, mate gap stddev=27.1141, read length mean=130.51)
[2026-05-28T00:06:35] Filtering read-through fragments with a distance <=10000bp (remaining=1607750)
[2026-05-28T00:06:35] Filtering inconsistently clipped mates (remaining=1576268)
[2026-05-28T00:06:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1526175)
[2026-05-28T00:06:37] Filtering fragments with small insert size (remaining=1525797)
[2026-05-28T00:06:38] Filtering alignments with long gaps (remaining=1525797)
[2026-05-28T00:06:39] Filtering fragments with both mates in the same gene (remaining=1525457)
[2026-05-28T00:06:39] Filtering fusions arising from hairpin structures (remaining=1438005)
[2026-05-28T00:06:40] Filtering reads with a mismatch p-value <=0.01 (remaining=634838)
[2026-05-28T00:06:44] Filtering reads with low entropy (k-mer content >=60%) (remaining=327833)
[2026-05-28T00:06:47] Finding fusions and counting supporting reads (total=286101)
[2026-05-28T00:06:54] Merging adjacent fusion breakpoints (remaining=283214)
[2026-05-28T00:06:54] Filtering multi-mapping fusions by alignment score and read support (remaining=161952)
[2026-05-28T00:07:06] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:07:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=161061)
[2026-05-28T00:07:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=83586)
[2026-05-28T00:07:09] Filtering fusions with <2 supporting reads (remaining=9862)
[2026-05-28T00:07:09] Filtering fusions with an e-value >=0.3 (remaining=2868)
[2026-05-28T00:07:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2904)
[2026-05-28T00:07:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2878)
[2026-05-28T00:07:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2878)
[2026-05-28T00:07:12] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2783)
[2026-05-28T00:07:13] Searching for fusions with spliced split reads (remaining=2803)
[2026-05-28T00:07:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=2070)
[2026-05-28T00:07:16] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2054)
[2026-05-28T00:07:16] Searching for fusions with >=4 spliced events (remaining=2243)
[2026-05-28T00:07:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=697)
[2026-05-28T00:07:28] Filtering fusions with anchors <=23nt (remaining=597)
[2026-05-28T00:07:28] Filtering end-to-end fusions with low support (remaining=570)
[2026-05-28T00:07:28] Filtering fusions with no coverage around the breakpoints (remaining=554)
[2026-05-28T00:07:28] Indexing gene sequences 
[2026-05-28T00:07:31] Filtering genes with >=30% identity (remaining=198)
[2026-05-28T00:07:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=96)
[2026-05-28T00:07:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=94)
[2026-05-28T00:07:34] Searching for additional isoforms (remaining=111)
[2026-05-28T00:07:34] Assigning confidence scores to events 
[2026-05-28T00:07:36] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:07:36] Writing fusions to file '659_djb-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:07:36] Writing discarded fusions to file '659_djb-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:07:48] Freeing resources
[2026-05-28T00:07:55] Done (elapsed time=00:04:05, CPU time=00:04:05, peak memory=7.79gb)