[2026-06-08T08:27:32] Launching Arriba 2.4.0
[2026-06-08T08:27:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:27:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:49] Reading chimeric alignments from '1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=14545098)
[2026-06-08T08:36:26] Marking multi-mapping alignments (marked=9407860)
[2026-06-08T08:36:33] Detecting strandedness (reverse)
[2026-06-08T08:36:33] Assigning strands to alignments 
[2026-06-08T08:36:36] Annotating alignments 
[2026-06-08T08:37:37] Filtering duplicates (remaining=10837058)
[2026-06-08T08:37:50] 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=9977797)
[2026-06-08T08:37:53] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9977797)
[2026-06-08T08:37:56] Filtering viral contigs with expression lower than the top 5 (remaining=9977797)
[2026-06-08T08:38:04] Filtering viral contigs with less than 5% coverage (remaining=9977797)
[2026-06-08T08:38:07] Estimating fragment length (mate gap mean=-80.2663, mate gap stddev=26.173, read length mean=124.736)
[2026-06-08T08:38:08] Filtering read-through fragments with a distance <=10000bp (remaining=9701938)
[2026-06-08T08:38:11] Filtering inconsistently clipped mates (remaining=9566766)
[2026-06-08T08:38:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9391942)
[2026-06-08T08:38:22] Filtering fragments with small insert size (remaining=9390720)
[2026-06-08T08:38:25] Filtering alignments with long gaps (remaining=9390720)
[2026-06-08T08:38:28] Filtering fragments with both mates in the same gene (remaining=9389258)
[2026-06-08T08:38:32] Filtering fusions arising from hairpin structures (remaining=9040346)
[2026-06-08T08:38:35] Filtering reads with a mismatch p-value <=0.01 (remaining=5095870)
[2026-06-08T08:38:58] Filtering reads with low entropy (k-mer content >=60%) (remaining=2893732)
[2026-06-08T08:39:20] Finding fusions and counting supporting reads (total=2832561)
[2026-06-08T08:39:57] Merging adjacent fusion breakpoints (remaining=2824708)
[2026-06-08T08:40:01] Filtering multi-mapping fusions by alignment score and read support (remaining=1642207)
[2026-06-08T08:40:57] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1641114)
[2026-06-08T08:41:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1513885)
[2026-06-08T08:41:21] Filtering fusions with <2 supporting reads (remaining=26229)
[2026-06-08T08:41:23] Filtering fusions with an e-value >=0.3 (remaining=3772)
[2026-06-08T08:41:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3814)
[2026-06-08T08:41:32] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3722)
[2026-06-08T08:41:33] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3722)
[2026-06-08T08:41:38] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3709)
[2026-06-08T08:41:49] Searching for fusions with spliced split reads (remaining=3822)
[2026-06-08T08:42:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=2867)
[2026-06-08T08:42:04] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2828)
[2026-06-08T08:42:06] Searching for fusions with >=4 spliced events (remaining=3442)
[2026-06-08T08:42:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1421)
[2026-06-08T08:42:31] Filtering fusions with anchors <=23nt (remaining=1215)
[2026-06-08T08:42:33] Filtering end-to-end fusions with low support (remaining=1187)
[2026-06-08T08:42:35] Filtering fusions with no coverage around the breakpoints (remaining=1169)
[2026-06-08T08:42:37] Indexing gene sequences 
[2026-06-08T08:42:45] Filtering genes with >=30% identity (remaining=401)
[2026-06-08T08:42:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=194)
[2026-06-08T08:43:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=166)
[2026-06-08T08:43:03] Searching for additional isoforms (remaining=228)
[2026-06-08T08:43:07] Assigning confidence scores to events 
[2026-06-08T08:43:16] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:43:16] Writing fusions to file '1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:43:21] Writing discarded fusions to file '1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:44:48] Freeing resources
[2026-06-08T08:45:19] Done (elapsed time=00:17:47, CPU time=00:17:47, peak memory=19.6gb)