[2026-06-08T08:45:33] Launching Arriba 2.4.0
[2026-06-08T08:45:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:45:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:45:46] Reading chimeric alignments from '1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=15973694)
[2026-06-08T08:53:11] Marking multi-mapping alignments (marked=10329752)
[2026-06-08T08:53:16] Detecting strandedness (reverse)
[2026-06-08T08:53:16] Assigning strands to alignments 
[2026-06-08T08:53:19] Annotating alignments 
[2026-06-08T08:54:10] Filtering duplicates (remaining=11992845)
[2026-06-08T08:54:22] 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=11027010)
[2026-06-08T08:54:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=11027010)
[2026-06-08T08:54:28] Filtering viral contigs with expression lower than the top 5 (remaining=11027010)
[2026-06-08T08:54:36] Filtering viral contigs with less than 5% coverage (remaining=11027010)
[2026-06-08T08:54:39] Estimating fragment length (mate gap mean=-83.6433, mate gap stddev=28.2886, read length mean=131.805)
[2026-06-08T08:54:40] Filtering read-through fragments with a distance <=10000bp (remaining=10637858)
[2026-06-08T08:54:43] Filtering inconsistently clipped mates (remaining=10484892)
[2026-06-08T08:54:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=10310060)
[2026-06-08T08:54:52] Filtering fragments with small insert size (remaining=10308889)
[2026-06-08T08:54:55] Filtering alignments with long gaps (remaining=10308889)
[2026-06-08T08:54:59] Filtering fragments with both mates in the same gene (remaining=10307473)
[2026-06-08T08:55:02] Filtering fusions arising from hairpin structures (remaining=9865192)
[2026-06-08T08:55:06] Filtering reads with a mismatch p-value <=0.01 (remaining=5398492)
[2026-06-08T08:55:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=2933910)
[2026-06-08T08:55:49] Finding fusions and counting supporting reads (total=2796400)
[2026-06-08T08:56:18] Merging adjacent fusion breakpoints (remaining=2787058)
[2026-06-08T08:56:22] Filtering multi-mapping fusions by alignment score and read support (remaining=1608386)
[2026-06-08T08:57:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:29] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1606266)
[2026-06-08T08:57:31] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1399663)
[2026-06-08T08:57:33] Filtering fusions with <2 supporting reads (remaining=48356)
[2026-06-08T08:57:34] Filtering fusions with an e-value >=0.3 (remaining=7213)
[2026-06-08T08:57:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7311)
[2026-06-08T08:57:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7235)
[2026-06-08T08:57:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7253)
[2026-06-08T08:57:47] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5858)
[2026-06-08T08:57:57] Searching for fusions with spliced split reads (remaining=5992)
[2026-06-08T08:58:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=3979)
[2026-06-08T08:58:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3902)
[2026-06-08T08:58:11] Searching for fusions with >=4 spliced events (remaining=4829)
[2026-06-08T08:58:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1837)
[2026-06-08T08:58:30] Filtering fusions with anchors <=23nt (remaining=1450)
[2026-06-08T08:58:31] Filtering end-to-end fusions with low support (remaining=1424)
[2026-06-08T08:58:33] Filtering fusions with no coverage around the breakpoints (remaining=1403)
[2026-06-08T08:58:34] Indexing gene sequences 
[2026-06-08T08:58:41] Filtering genes with >=30% identity (remaining=496)
[2026-06-08T08:58:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=270)
[2026-06-08T08:58:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=228)
[2026-06-08T08:58:53] Searching for additional isoforms (remaining=292)
[2026-06-08T08:58:56] Assigning confidence scores to events 
[2026-06-08T08:59:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:03] Writing fusions to file '1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:59:05] Writing discarded fusions to file '1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:01] Freeing resources
[2026-06-08T09:00:26] Done (elapsed time=00:14:53, CPU time=00:14:52, peak memory=21.1gb)