[2026-06-08T08:34:33] Launching Arriba 2.4.0
[2026-06-08T08:34:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:34:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:34:45] Reading chimeric alignments from '1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=13608835)
[2026-06-08T08:42:13] Marking multi-mapping alignments (marked=8323212)
[2026-06-08T08:42:18] Detecting strandedness (reverse)
[2026-06-08T08:42:18] Assigning strands to alignments 
[2026-06-08T08:42:21] Annotating alignments 
[2026-06-08T08:43:06] Filtering duplicates (remaining=10541461)
[2026-06-08T08:43:17] 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=9826048)
[2026-06-08T08:43:20] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9826048)
[2026-06-08T08:43:22] Filtering viral contigs with expression lower than the top 5 (remaining=9826048)
[2026-06-08T08:43:29] Filtering viral contigs with less than 5% coverage (remaining=9826048)
[2026-06-08T08:43:32] Estimating fragment length (mate gap mean=-83.4112, mate gap stddev=28.2905, read length mean=133.636)
[2026-06-08T08:43:32] Filtering read-through fragments with a distance <=10000bp (remaining=9487982)
[2026-06-08T08:43:35] Filtering inconsistently clipped mates (remaining=9373435)
[2026-06-08T08:43:37] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9224593)
[2026-06-08T08:43:44] Filtering fragments with small insert size (remaining=9223727)
[2026-06-08T08:43:46] Filtering alignments with long gaps (remaining=9223726)
[2026-06-08T08:43:49] Filtering fragments with both mates in the same gene (remaining=9222538)
[2026-06-08T08:43:52] Filtering fusions arising from hairpin structures (remaining=8904432)
[2026-06-08T08:43:55] Filtering reads with a mismatch p-value <=0.01 (remaining=4976046)
[2026-06-08T08:44:18] Filtering reads with low entropy (k-mer content >=60%) (remaining=2852206)
[2026-06-08T08:44:37] Finding fusions and counting supporting reads (total=2640124)
[2026-06-08T08:45:04] Merging adjacent fusion breakpoints (remaining=2632652)
[2026-06-08T08:45:07] Filtering multi-mapping fusions by alignment score and read support (remaining=1658262)
[2026-06-08T08:45:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:46:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1656965)
[2026-06-08T08:46:11] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1454169)
[2026-06-08T08:46:12] Filtering fusions with <2 supporting reads (remaining=66810)
[2026-06-08T08:46:14] Filtering fusions with an e-value >=0.3 (remaining=6579)
[2026-06-08T08:46:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6657)
[2026-06-08T08:46:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6618)
[2026-06-08T08:46:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6620)
[2026-06-08T08:46:25] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5189)
[2026-06-08T08:46:34] Searching for fusions with spliced split reads (remaining=5272)
[2026-06-08T08:46:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=3565)
[2026-06-08T08:46:45] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3531)
[2026-06-08T08:46:46] Searching for fusions with >=4 spliced events (remaining=4679)
[2026-06-08T08:46:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1977)
[2026-06-08T08:47:02] Filtering fusions with anchors <=23nt (remaining=1690)
[2026-06-08T08:47:03] Filtering end-to-end fusions with low support (remaining=1671)
[2026-06-08T08:47:05] Filtering fusions with no coverage around the breakpoints (remaining=1643)
[2026-06-08T08:47:06] Indexing gene sequences 
[2026-06-08T08:47:13] Filtering genes with >=30% identity (remaining=626)
[2026-06-08T08:47:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=408)
[2026-06-08T08:47:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=257)
[2026-06-08T08:47:51] Searching for additional isoforms (remaining=581)
[2026-06-08T08:47:53] Assigning confidence scores to events 
[2026-06-08T08:48:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:48:00] Writing fusions to file '1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:48:05] Writing discarded fusions to file '1173_D6K_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:48:59] Freeing resources
[2026-06-08T08:49:23] Done (elapsed time=00:14:50, CPU time=00:14:49, peak memory=18.5gb)