[2026-05-28T00:03:03] Launching Arriba 2.4.0
[2026-05-28T00:03:03] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:03:11] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:03:15] Reading chimeric alignments from '659_d01-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3424607)
[2026-05-28T00:05:25] Marking multi-mapping alignments (marked=2199872)
[2026-05-28T00:05:27] Detecting strandedness (reverse)
[2026-05-28T00:05:27] Assigning strands to alignments 
[2026-05-28T00:05:27] Annotating alignments 
[2026-05-28T00:05:40] Filtering duplicates (remaining=1751260)
[2026-05-28T00:05:41] 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=1655054)
[2026-05-28T00:05:42] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1655054)
[2026-05-28T00:05:43] Filtering viral contigs with expression lower than the top 5 (remaining=1655054)
[2026-05-28T00:05:44] Filtering viral contigs with less than 5% coverage (remaining=1655054)
[2026-05-28T00:05:45] Estimating fragment length (mate gap mean=-85.7021, mate gap stddev=28.7526, read length mean=131.242)
[2026-05-28T00:05:45] Filtering read-through fragments with a distance <=10000bp (remaining=1565366)
[2026-05-28T00:05:46] Filtering inconsistently clipped mates (remaining=1538582)
[2026-05-28T00:05:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1483317)
[2026-05-28T00:05:48] Filtering fragments with small insert size (remaining=1482975)
[2026-05-28T00:05:48] Filtering alignments with long gaps (remaining=1482974)
[2026-05-28T00:05:49] Filtering fragments with both mates in the same gene (remaining=1482611)
[2026-05-28T00:05:49] Filtering fusions arising from hairpin structures (remaining=1404310)
[2026-05-28T00:05:50] Filtering reads with a mismatch p-value <=0.01 (remaining=616803)
[2026-05-28T00:05:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=224107)
[2026-05-28T00:05:57] Finding fusions and counting supporting reads (total=201579)
[2026-05-28T00:06:03] Merging adjacent fusion breakpoints (remaining=200559)
[2026-05-28T00:06:03] Filtering multi-mapping fusions by alignment score and read support (remaining=120345)
[2026-05-28T00:06:14] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:06:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=119347)
[2026-05-28T00:06:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=62635)
[2026-05-28T00:06:17] Filtering fusions with <2 supporting reads (remaining=6356)
[2026-05-28T00:06:17] Filtering fusions with an e-value >=0.3 (remaining=1980)
[2026-05-28T00:06:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2014)
[2026-05-28T00:06:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1968)
[2026-05-28T00:06:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1969)
[2026-05-28T00:06:19] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1819)
[2026-05-28T00:06:21] Searching for fusions with spliced split reads (remaining=1852)
[2026-05-28T00:06:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=1389)
[2026-05-28T00:06:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1355)
[2026-05-28T00:06:23] Searching for fusions with >=4 spliced events (remaining=1487)
[2026-05-28T00:06:24] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=419)
[2026-05-28T00:06:35] Filtering fusions with anchors <=23nt (remaining=341)
[2026-05-28T00:06:35] Filtering end-to-end fusions with low support (remaining=331)
[2026-05-28T00:06:35] Filtering fusions with no coverage around the breakpoints (remaining=316)
[2026-05-28T00:06:36] Indexing gene sequences 
[2026-05-28T00:06:38] Filtering genes with >=30% identity (remaining=130)
[2026-05-28T00:06:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=84)
[2026-05-28T00:06:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=79)
[2026-05-28T00:06:40] Searching for additional isoforms (remaining=91)
[2026-05-28T00:06:40] Assigning confidence scores to events 
[2026-05-28T00:06:41] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:06:41] Writing fusions to file '659_d01-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:06:42] Writing discarded fusions to file '659_d01-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:06:52] Freeing resources
[2026-05-28T00:06:59] Done (elapsed time=00:03:56, CPU time=00:03:56, peak memory=7.66gb)