[2026-06-08T08:11:58] Launching Arriba 2.4.0
[2026-06-08T08:11:58] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:12:13] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:12:17] Reading chimeric alignments from '659_Mt-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=6799830)
[2026-06-08T08:16:43] Marking multi-mapping alignments (marked=4464180)
[2026-06-08T08:16:46] Detecting strandedness (no)
[2026-06-08T08:16:46] Annotating alignments 
[2026-06-08T08:17:09] Filtering duplicates (remaining=1784821)
[2026-06-08T08:17:12] 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=1655367)
[2026-06-08T08:17:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1655367)
[2026-06-08T08:17:14] Filtering viral contigs with expression lower than the top 5 (remaining=1655367)
[2026-06-08T08:17:16] Filtering viral contigs with less than 5% coverage (remaining=1655367)
[2026-06-08T08:17:18] Estimating fragment length (mate gap mean=-85.7731, mate gap stddev=28.3206, read length mean=127.883)
[2026-06-08T08:17:18] Filtering read-through fragments with a distance <=10000bp (remaining=1583622)
[2026-06-08T08:17:19] Filtering inconsistently clipped mates (remaining=1551338)
[2026-06-08T08:17:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1465654)
[2026-06-08T08:17:22] Filtering fragments with small insert size (remaining=1465388)
[2026-06-08T08:17:23] Filtering alignments with long gaps (remaining=1465387)
[2026-06-08T08:17:24] Filtering fragments with both mates in the same gene (remaining=1464987)
[2026-06-08T08:17:25] Filtering fusions arising from hairpin structures (remaining=1401989)
[2026-06-08T08:17:26] Filtering reads with a mismatch p-value <=0.01 (remaining=571699)
[2026-06-08T08:17:30] Filtering reads with low entropy (k-mer content >=60%) (remaining=197973)
[2026-06-08T08:17:34] Finding fusions and counting supporting reads (total=169415)
[2026-06-08T08:17:41] Merging adjacent fusion breakpoints (remaining=168294)
[2026-06-08T08:17:41] Filtering multi-mapping fusions by alignment score and read support (remaining=86642)
[2026-06-08T08:17:59] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:18:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=86001)
[2026-06-08T08:18:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=54351)
[2026-06-08T08:18:02] Filtering fusions with <2 supporting reads (remaining=5475)
[2026-06-08T08:18:02] Filtering fusions with an e-value >=0.3 (remaining=1288)
[2026-06-08T08:18:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1306)
[2026-06-08T08:18:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1250)
[2026-06-08T08:18:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1250)
[2026-06-08T08:18:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1184)
[2026-06-08T08:18:06] Searching for fusions with spliced split reads (remaining=1313)
[2026-06-08T08:18:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=1024)
[2026-06-08T08:18:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1013)
[2026-06-08T08:18:09] Searching for fusions with >=4 spliced events (remaining=1113)
[2026-06-08T08:18:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=303)
[2026-06-08T08:18:21] Filtering fusions with anchors <=23nt (remaining=270)
[2026-06-08T08:18:22] Filtering end-to-end fusions with low support (remaining=260)
[2026-06-08T08:18:22] Filtering fusions with no coverage around the breakpoints (remaining=250)
[2026-06-08T08:18:22] Indexing gene sequences 
[2026-06-08T08:18:24] Filtering genes with >=30% identity (remaining=80)
[2026-06-08T08:18:24] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=43)
[2026-06-08T08:18:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=43)
[2026-06-08T08:18:25] Searching for additional isoforms (remaining=50)
[2026-06-08T08:18:25] Assigning confidence scores to events 
[2026-06-08T08:18:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:18:26] Writing fusions to file '659_Mt-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:18:26] Writing discarded fusions to file '659_Mt-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:18:34] Freeing resources
[2026-06-08T08:18:44] Done (elapsed time=00:06:46, CPU time=00:06:44, peak memory=11gb)