[2026-06-08T08:41:02] Launching Arriba 2.4.0
[2026-06-08T08:41:02] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:41:21] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:41:27] Reading chimeric alignments from '1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=18956047)
[2026-06-08T08:53:37] Marking multi-mapping alignments (marked=13949285)
[2026-06-08T08:53:44] Detecting strandedness (reverse)
[2026-06-08T08:53:44] Assigning strands to alignments 
[2026-06-08T08:53:49] Annotating alignments 
[2026-06-08T08:54:59] Filtering duplicates (remaining=6932970)
[2026-06-08T08:55:14] 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=6161147)
[2026-06-08T08:55:18] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6161147)
[2026-06-08T08:55:22] Filtering viral contigs with expression lower than the top 5 (remaining=6161147)
[2026-06-08T08:55:31] Filtering viral contigs with less than 5% coverage (remaining=6161147)
[2026-06-08T08:55:35] Estimating fragment length (mate gap mean=-78.8726, mate gap stddev=27.9451, read length mean=115.885)
[2026-06-08T08:55:35] Filtering read-through fragments with a distance <=10000bp (remaining=5973411)
[2026-06-08T08:55:39] Filtering inconsistently clipped mates (remaining=5844907)
[2026-06-08T08:55:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5729470)
[2026-06-08T08:55:48] Filtering fragments with small insert size (remaining=5726821)
[2026-06-08T08:55:52] Filtering alignments with long gaps (remaining=5726821)
[2026-06-08T08:55:56] Filtering fragments with both mates in the same gene (remaining=5725716)
[2026-06-08T08:56:00] Filtering fusions arising from hairpin structures (remaining=5428839)
[2026-06-08T08:56:05] Filtering reads with a mismatch p-value <=0.01 (remaining=2120201)
[2026-06-08T08:56:20] Filtering reads with low entropy (k-mer content >=60%) (remaining=690116)
[2026-06-08T08:56:33] Finding fusions and counting supporting reads (total=595005)
[2026-06-08T08:57:03] Merging adjacent fusion breakpoints (remaining=588441)
[2026-06-08T08:57:05] Filtering multi-mapping fusions by alignment score and read support (remaining=291290)
[2026-06-08T08:58:15] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:25] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=290206)
[2026-06-08T08:58:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=197596)
[2026-06-08T08:58:26] Filtering fusions with <2 supporting reads (remaining=13225)
[2026-06-08T08:58:27] Filtering fusions with an e-value >=0.3 (remaining=2754)
[2026-06-08T08:58:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2815)
[2026-06-08T08:58:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2730)
[2026-06-08T08:58:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2730)
[2026-06-08T08:58:37] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2720)
[2026-06-08T08:58:47] Searching for fusions with spliced split reads (remaining=2786)
[2026-06-08T08:58:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=2023)
[2026-06-08T08:59:00] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2008)
[2026-06-08T08:59:01] Searching for fusions with >=4 spliced events (remaining=2296)
[2026-06-08T08:59:02] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=964)
[2026-06-08T08:59:25] Filtering fusions with anchors <=23nt (remaining=825)
[2026-06-08T08:59:26] Filtering end-to-end fusions with low support (remaining=787)
[2026-06-08T08:59:26] Filtering fusions with no coverage around the breakpoints (remaining=755)
[2026-06-08T08:59:27] Indexing gene sequences 
[2026-06-08T08:59:33] Filtering genes with >=30% identity (remaining=293)
[2026-06-08T08:59:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=166)
[2026-06-08T08:59:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=139)
[2026-06-08T08:59:39] Searching for additional isoforms (remaining=151)
[2026-06-08T08:59:40] Assigning confidence scores to events 
[2026-06-08T08:59:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:44] Writing fusions to file '1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:59:46] Writing discarded fusions to file '1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:45] Freeing resources
[2026-06-08T09:01:28] Done (elapsed time=00:20:26, CPU time=00:20:25, peak memory=22.9gb)