[2026-06-08T08:37:33] Launching Arriba 2.4.0
[2026-06-08T08:37:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:37:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:37:45] Reading chimeric alignments from '1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=13679611)
[2026-06-08T08:45:22] Marking multi-mapping alignments (marked=8574087)
[2026-06-08T08:45:28] Detecting strandedness (reverse)
[2026-06-08T08:45:28] Assigning strands to alignments 
[2026-06-08T08:45:30] Annotating alignments 
[2026-06-08T08:46:19] Filtering duplicates (remaining=10877448)
[2026-06-08T08:46:31] 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=9664083)
[2026-06-08T08:46:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9664083)
[2026-06-08T08:46:36] Filtering viral contigs with expression lower than the top 5 (remaining=9664083)
[2026-06-08T08:46:45] Filtering viral contigs with less than 5% coverage (remaining=9664083)
[2026-06-08T08:46:48] Estimating fragment length (mate gap mean=-82.9739, mate gap stddev=27.7198, read length mean=131.187)
[2026-06-08T08:46:49] Filtering read-through fragments with a distance <=10000bp (remaining=9399715)
[2026-06-08T08:46:52] Filtering inconsistently clipped mates (remaining=9333247)
[2026-06-08T08:46:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9185796)
[2026-06-08T08:47:02] Filtering fragments with small insert size (remaining=9185015)
[2026-06-08T08:47:05] Filtering alignments with long gaps (remaining=9185014)
[2026-06-08T08:47:08] Filtering fragments with both mates in the same gene (remaining=9183633)
[2026-06-08T08:47:11] Filtering fusions arising from hairpin structures (remaining=9009188)
[2026-06-08T08:47:14] Filtering reads with a mismatch p-value <=0.01 (remaining=5226293)
[2026-06-08T08:47:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=3256612)
[2026-06-08T08:47:59] Finding fusions and counting supporting reads (total=3156145)
[2026-06-08T08:48:28] Merging adjacent fusion breakpoints (remaining=3150240)
[2026-06-08T08:48:32] Filtering multi-mapping fusions by alignment score and read support (remaining=1868889)
[2026-06-08T08:49:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:38] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1867891)
[2026-06-08T08:49:40] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1720534)
[2026-06-08T08:49:42] Filtering fusions with <2 supporting reads (remaining=55295)
[2026-06-08T08:49:43] Filtering fusions with an e-value >=0.3 (remaining=5029)
[2026-06-08T08:49:44] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5074)
[2026-06-08T08:49:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5039)
[2026-06-08T08:49:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5041)
[2026-06-08T08:49:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4226)
[2026-06-08T08:50:07] Searching for fusions with spliced split reads (remaining=4299)
[2026-06-08T08:50:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=3023)
[2026-06-08T08:50:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3007)
[2026-06-08T08:50:19] Searching for fusions with >=4 spliced events (remaining=3838)
[2026-06-08T08:50:22] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1543)
[2026-06-08T08:50:35] Filtering fusions with anchors <=23nt (remaining=1251)
[2026-06-08T08:50:37] Filtering end-to-end fusions with low support (remaining=1237)
[2026-06-08T08:50:38] Filtering fusions with no coverage around the breakpoints (remaining=1214)
[2026-06-08T08:50:40] Indexing gene sequences 
[2026-06-08T08:50:46] Filtering genes with >=30% identity (remaining=528)
[2026-06-08T08:51:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=365)
[2026-06-08T08:51:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=240)
[2026-06-08T08:51:19] Searching for additional isoforms (remaining=553)
[2026-06-08T08:51:22] Assigning confidence scores to events 
[2026-06-08T08:51:28] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:51:28] Writing fusions to file '1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:51:33] Writing discarded fusions to file '1173_D6K_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:52:41] Freeing resources
[2026-06-08T08:53:06] Done (elapsed time=00:15:33, CPU time=00:15:32, peak memory=19gb)