[2026-06-08T08:24:22] Launching Arriba 2.4.0
[2026-06-08T08:24:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:24:34] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:24:38] Reading chimeric alignments from '1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=13788997)
[2026-06-08T08:30:54] Marking multi-mapping alignments (marked=8805167)
[2026-06-08T08:31:00] Detecting strandedness (reverse)
[2026-06-08T08:31:00] Assigning strands to alignments 
[2026-06-08T08:31:03] Annotating alignments 
[2026-06-08T08:31:45] Filtering duplicates (remaining=9750829)
[2026-06-08T08:31:55] 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=9255284)
[2026-06-08T08:31:58] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9255284)
[2026-06-08T08:32:01] Filtering viral contigs with expression lower than the top 5 (remaining=9255284)
[2026-06-08T08:32:07] Filtering viral contigs with less than 5% coverage (remaining=9255284)
[2026-06-08T08:32:10] Estimating fragment length (mate gap mean=-80.4963, mate gap stddev=26.8354, read length mean=128.1)
[2026-06-08T08:32:10] Filtering read-through fragments with a distance <=10000bp (remaining=8995339)
[2026-06-08T08:32:13] Filtering inconsistently clipped mates (remaining=8840848)
[2026-06-08T08:32:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=8719203)
[2026-06-08T08:32:22] Filtering fragments with small insert size (remaining=8718082)
[2026-06-08T08:32:25] Filtering alignments with long gaps (remaining=8718081)
[2026-06-08T08:32:28] Filtering fragments with both mates in the same gene (remaining=8716949)
[2026-06-08T08:32:31] Filtering fusions arising from hairpin structures (remaining=8300327)
[2026-06-08T08:32:34] Filtering reads with a mismatch p-value <=0.01 (remaining=4538322)
[2026-06-08T08:32:55] Filtering reads with low entropy (k-mer content >=60%) (remaining=2321623)
[2026-06-08T08:33:13] Finding fusions and counting supporting reads (total=2223990)
[2026-06-08T08:33:36] Merging adjacent fusion breakpoints (remaining=2216496)
[2026-06-08T08:33:39] Filtering multi-mapping fusions by alignment score and read support (remaining=1374154)
[2026-06-08T08:34:18] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:34:29] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1373122)
[2026-06-08T08:34:31] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1233857)
[2026-06-08T08:34:32] Filtering fusions with <2 supporting reads (remaining=25366)
[2026-06-08T08:34:33] Filtering fusions with an e-value >=0.3 (remaining=3648)
[2026-06-08T08:34:34] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3720)
[2026-06-08T08:34:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3654)
[2026-06-08T08:34:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3654)
[2026-06-08T08:34:43] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3627)
[2026-06-08T08:34:50] Searching for fusions with spliced split reads (remaining=3751)
[2026-06-08T08:34:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=2737)
[2026-06-08T08:35:00] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2697)
[2026-06-08T08:35:01] Searching for fusions with >=4 spliced events (remaining=3407)
[2026-06-08T08:35:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1450)
[2026-06-08T08:35:16] Filtering fusions with anchors <=23nt (remaining=1274)
[2026-06-08T08:35:17] Filtering end-to-end fusions with low support (remaining=1252)
[2026-06-08T08:35:18] Filtering fusions with no coverage around the breakpoints (remaining=1233)
[2026-06-08T08:35:19] Indexing gene sequences 
[2026-06-08T08:35:24] Filtering genes with >=30% identity (remaining=355)
[2026-06-08T08:35:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=170)
[2026-06-08T08:35:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=156)
[2026-06-08T08:35:35] Searching for additional isoforms (remaining=202)
[2026-06-08T08:35:37] Assigning confidence scores to events 
[2026-06-08T08:35:42] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:35:42] Writing fusions to file '1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:35:44] Writing discarded fusions to file '1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:36:29] Freeing resources
[2026-06-08T08:36:52] Done (elapsed time=00:12:30, CPU time=00:12:29, peak memory=18.5gb)