[2026-06-08T08:19:25] Launching Arriba 2.4.0
[2026-06-08T08:19:25] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:19:34] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:19:38] Reading chimeric alignments from '1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=14486800)
[2026-06-08T08:26:31] Marking multi-mapping alignments (marked=11193842)
[2026-06-08T08:26:38] Detecting strandedness (reverse)
[2026-06-08T08:26:38] Assigning strands to alignments 
[2026-06-08T08:26:41] Annotating alignments 
[2026-06-08T08:27:47] Filtering duplicates (remaining=8638024)
[2026-06-08T08:28:00] 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=6776537)
[2026-06-08T08:28:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6776537)
[2026-06-08T08:28:07] Filtering viral contigs with expression lower than the top 5 (remaining=6776537)
[2026-06-08T08:28:15] Filtering viral contigs with less than 5% coverage (remaining=6776537)
[2026-06-08T08:28:19] Estimating fragment length (mate gap mean=-76.5508, mate gap stddev=28.7097, read length mean=109.199)
[2026-06-08T08:28:19] Filtering read-through fragments with a distance <=10000bp (remaining=6651090)
[2026-06-08T08:28:22] Filtering inconsistently clipped mates (remaining=6583869)
[2026-06-08T08:28:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6410977)
[2026-06-08T08:28:32] Filtering fragments with small insert size (remaining=6409825)
[2026-06-08T08:28:35] Filtering alignments with long gaps (remaining=6409824)
[2026-06-08T08:28:38] Filtering fragments with both mates in the same gene (remaining=6408392)
[2026-06-08T08:28:42] Filtering fusions arising from hairpin structures (remaining=6292909)
[2026-06-08T08:28:46] Filtering reads with a mismatch p-value <=0.01 (remaining=2516395)
[2026-06-08T08:29:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=1030776)
[2026-06-08T08:29:12] Finding fusions and counting supporting reads (total=973476)
[2026-06-08T08:29:44] Merging adjacent fusion breakpoints (remaining=970904)
[2026-06-08T08:29:47] Filtering multi-mapping fusions by alignment score and read support (remaining=415135)
[2026-06-08T08:30:40] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:30:54] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=413971)
[2026-06-08T08:30:56] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=364752)
[2026-06-08T08:30:57] Filtering fusions with <2 supporting reads (remaining=12938)
[2026-06-08T08:30:59] Filtering fusions with an e-value >=0.3 (remaining=2655)
[2026-06-08T08:31:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2683)
[2026-06-08T08:31:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2641)
[2026-06-08T08:31:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2642)
[2026-06-08T08:31:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2640)
[2026-06-08T08:31:20] Searching for fusions with spliced split reads (remaining=2759)
[2026-06-08T08:31:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=2107)
[2026-06-08T08:31:32] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2082)
[2026-06-08T08:31:34] Searching for fusions with >=4 spliced events (remaining=2268)
[2026-06-08T08:31:36] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=963)
[2026-06-08T08:31:52] Filtering fusions with anchors <=23nt (remaining=629)
[2026-06-08T08:31:54] Filtering end-to-end fusions with low support (remaining=616)
[2026-06-08T08:31:55] Filtering fusions with no coverage around the breakpoints (remaining=598)
[2026-06-08T08:31:56] Indexing gene sequences 
[2026-06-08T08:32:02] Filtering genes with >=30% identity (remaining=250)
[2026-06-08T08:32:04] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=143)
[2026-06-08T08:32:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=127)
[2026-06-08T08:32:11] Searching for additional isoforms (remaining=148)
[2026-06-08T08:32:13] Assigning confidence scores to events 
[2026-06-08T08:32:19] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:32:19] Writing fusions to file '1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:32:21] Writing discarded fusions to file '1173_IT6_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:33:18] Freeing resources
[2026-06-08T08:33:44] Done (elapsed time=00:14:19, CPU time=00:14:17, peak memory=19.3gb)