[2026-05-28T00:03:54] Launching Arriba 2.4.0
[2026-05-28T00:03:54] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:04:03] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:04:07] Reading chimeric alignments from '659_gK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3330783)
[2026-05-28T00:06:19] Marking multi-mapping alignments (marked=2150153)
[2026-05-28T00:06:20] Detecting strandedness (reverse)
[2026-05-28T00:06:20] Assigning strands to alignments 
[2026-05-28T00:06:21] Annotating alignments 
[2026-05-28T00:06:31] Filtering duplicates (remaining=1753822)
[2026-05-28T00:06:33] 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=1698095)
[2026-05-28T00:06:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1698095)
[2026-05-28T00:06:34] Filtering viral contigs with expression lower than the top 5 (remaining=1698095)
[2026-05-28T00:06:35] Filtering viral contigs with less than 5% coverage (remaining=1698095)
[2026-05-28T00:06:36] Estimating fragment length (mate gap mean=-85.5628, mate gap stddev=29.7335, read length mean=136.358)
[2026-05-28T00:06:36] Filtering read-through fragments with a distance <=10000bp (remaining=1600495)
[2026-05-28T00:06:37] Filtering inconsistently clipped mates (remaining=1578385)
[2026-05-28T00:06:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1526164)
[2026-05-28T00:06:39] Filtering fragments with small insert size (remaining=1525994)
[2026-05-28T00:06:39] Filtering alignments with long gaps (remaining=1525993)
[2026-05-28T00:06:40] Filtering fragments with both mates in the same gene (remaining=1525677)
[2026-05-28T00:06:41] Filtering fusions arising from hairpin structures (remaining=1453503)
[2026-05-28T00:06:41] Filtering reads with a mismatch p-value <=0.01 (remaining=659605)
[2026-05-28T00:06:45] Filtering reads with low entropy (k-mer content >=60%) (remaining=232919)
[2026-05-28T00:06:48] Finding fusions and counting supporting reads (total=198557)
[2026-05-28T00:06:52] Merging adjacent fusion breakpoints (remaining=197240)
[2026-05-28T00:06:53] Filtering multi-mapping fusions by alignment score and read support (remaining=119700)
[2026-05-28T00:07:03] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:07:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=118760)
[2026-05-28T00:07:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=60922)
[2026-05-28T00:07:06] Filtering fusions with <2 supporting reads (remaining=7373)
[2026-05-28T00:07:06] Filtering fusions with an e-value >=0.3 (remaining=2608)
[2026-05-28T00:07:06] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2633)
[2026-05-28T00:07:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2614)
[2026-05-28T00:07:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2618)
[2026-05-28T00:07:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1906)
[2026-05-28T00:07:10] Searching for fusions with spliced split reads (remaining=2065)
[2026-05-28T00:07:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=1496)
[2026-05-28T00:07:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1485)
[2026-05-28T00:07:12] Searching for fusions with >=4 spliced events (remaining=1604)
[2026-05-28T00:07:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=426)
[2026-05-28T00:07:23] Filtering fusions with anchors <=23nt (remaining=329)
[2026-05-28T00:07:24] Filtering end-to-end fusions with low support (remaining=322)
[2026-05-28T00:07:24] Filtering fusions with no coverage around the breakpoints (remaining=307)
[2026-05-28T00:07:24] Indexing gene sequences 
[2026-05-28T00:07:26] Filtering genes with >=30% identity (remaining=104)
[2026-05-28T00:07:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=50)
[2026-05-28T00:07:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=46)
[2026-05-28T00:07:28] Searching for additional isoforms (remaining=57)
[2026-05-28T00:07:29] Assigning confidence scores to events 
[2026-05-28T00:07:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:07:30] Writing fusions to file '659_gK-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:07:30] Writing discarded fusions to file '659_gK-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:07:39] Freeing resources
[2026-05-28T00:07:46] Done (elapsed time=00:03:52, CPU time=00:03:50, peak memory=7.53gb)