[2026-06-08T07:34:57] Launching Arriba 2.4.0
[2026-06-08T07:34:57] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:35:15] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:35:21] Reading chimeric alignments from '1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=13893382)
[2026-06-08T07:39:32] Marking multi-mapping alignments (marked=12672108)
[2026-06-08T07:39:37] Detecting strandedness (reverse)
[2026-06-08T07:39:37] Assigning strands to alignments 
[2026-06-08T07:39:39] Annotating alignments 
[2026-06-08T07:40:33] Filtering duplicates (remaining=7614126)
[2026-06-08T07:40:45] 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=3869738)
[2026-06-08T07:40:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3869738)
[2026-06-08T07:40:50] Filtering viral contigs with expression lower than the top 5 (remaining=3869738)
[2026-06-08T07:40:56] Filtering viral contigs with less than 5% coverage (remaining=3869738)
[2026-06-08T07:40:59] Estimating fragment length (mate gap mean=-48.2242, mate gap stddev=30.4922, read length mean=74.9389)
[2026-06-08T07:40:59] Filtering read-through fragments with a distance <=10000bp (remaining=3815147)
[2026-06-08T07:41:01] Filtering inconsistently clipped mates (remaining=3794585)
[2026-06-08T07:41:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3630617)
[2026-06-08T07:41:08] Filtering fragments with small insert size (remaining=3629990)
[2026-06-08T07:41:10] Filtering alignments with long gaps (remaining=3629990)
[2026-06-08T07:41:13] Filtering fragments with both mates in the same gene (remaining=3629323)
[2026-06-08T07:41:15] Filtering fusions arising from hairpin structures (remaining=3596251)
[2026-06-08T07:41:18] Filtering reads with a mismatch p-value <=0.01 (remaining=724908)
[2026-06-08T07:41:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=504620)
[2026-06-08T07:41:34] Finding fusions and counting supporting reads (total=492672)
[2026-06-08T07:41:59] Merging adjacent fusion breakpoints (remaining=489814)
[2026-06-08T07:42:02] Filtering multi-mapping fusions by alignment score and read support (remaining=125777)
[2026-06-08T07:42:43] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:42:52] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=121469)
[2026-06-08T07:42:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=119524)
[2026-06-08T07:42:54] Filtering fusions with <2 supporting reads (remaining=4170)
[2026-06-08T07:42:55] Filtering fusions with an e-value >=0.3 (remaining=845)
[2026-06-08T07:42:56] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=852)
[2026-06-08T07:43:00] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=816)
[2026-06-08T07:43:01] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=816)
[2026-06-08T07:43:03] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=806)
[2026-06-08T07:43:11] Searching for fusions with spliced split reads (remaining=817)
[2026-06-08T07:43:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=694)
[2026-06-08T07:43:20] Filtering read-through fusions with breakpoints near the gene boundary (remaining=692)
[2026-06-08T07:43:21] Searching for fusions with >=4 spliced events (remaining=700)
[2026-06-08T07:43:23] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=296)
[2026-06-08T07:43:45] Filtering fusions with anchors <=23nt (remaining=99)
[2026-06-08T07:43:46] Filtering end-to-end fusions with low support (remaining=98)
[2026-06-08T07:43:47] Filtering fusions with no coverage around the breakpoints (remaining=95)
[2026-06-08T07:43:48] Indexing gene sequences 
[2026-06-08T07:43:50] Filtering genes with >=30% identity (remaining=83)
[2026-06-08T07:43:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=76)
[2026-06-08T07:43:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=76)
[2026-06-08T07:43:55] Searching for additional isoforms (remaining=78)
[2026-06-08T07:43:57] Assigning confidence scores to events 
[2026-06-08T07:44:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:44:02] Writing fusions to file '1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:44:04] Writing discarded fusions to file '1173_JIG_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:44:52] Freeing resources
[2026-06-08T07:45:20] Done (elapsed time=00:10:23, CPU time=00:10:22, peak memory=19.1gb)