[2026-06-08T08:33:28] Launching Arriba 2.4.0
[2026-06-08T08:33:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:33:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:33:40] Reading chimeric alignments from '1173_KTN_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=11499861)
[2026-06-08T08:40:05] Marking multi-mapping alignments (marked=7991334)
[2026-06-08T08:40:09] Detecting strandedness (reverse)
[2026-06-08T08:40:09] Assigning strands to alignments 
[2026-06-08T08:40:12] Annotating alignments 
[2026-06-08T08:40:51] Filtering duplicates (remaining=6746616)
[2026-06-08T08:40:59] 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=6218037)
[2026-06-08T08:41:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6218037)
[2026-06-08T08:41:03] Filtering viral contigs with expression lower than the top 5 (remaining=6218037)
[2026-06-08T08:41:09] Filtering viral contigs with less than 5% coverage (remaining=6218037)
[2026-06-08T08:41:11] Estimating fragment length (mate gap mean=-79.0747, mate gap stddev=26.9446, read length mean=114.57)
[2026-06-08T08:41:11] Filtering read-through fragments with a distance <=10000bp (remaining=6046419)
[2026-06-08T08:41:14] Filtering inconsistently clipped mates (remaining=5973250)
[2026-06-08T08:41:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5823925)
[2026-06-08T08:41:20] Filtering fragments with small insert size (remaining=5822912)
[2026-06-08T08:41:22] Filtering alignments with long gaps (remaining=5822912)
[2026-06-08T08:41:25] Filtering fragments with both mates in the same gene (remaining=5821592)
[2026-06-08T08:41:27] Filtering fusions arising from hairpin structures (remaining=5670912)
[2026-06-08T08:41:30] Filtering reads with a mismatch p-value <=0.01 (remaining=2355765)
[2026-06-08T08:41:44] Filtering reads with low entropy (k-mer content >=60%) (remaining=829016)
[2026-06-08T08:41:53] Finding fusions and counting supporting reads (total=730555)
[2026-06-08T08:42:11] Merging adjacent fusion breakpoints (remaining=725202)
[2026-06-08T08:42:13] Filtering multi-mapping fusions by alignment score and read support (remaining=390628)
[2026-06-08T08:42:50] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:42:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=389797)
[2026-06-08T08:42:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=331406)
[2026-06-08T08:43:00] Filtering fusions with <2 supporting reads (remaining=16850)
[2026-06-08T08:43:00] Filtering fusions with an e-value >=0.3 (remaining=3369)
[2026-06-08T08:43:01] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3393)
[2026-06-08T08:43:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3330)
[2026-06-08T08:43:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3330)
[2026-06-08T08:43:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3329)
[2026-06-08T08:43:14] Searching for fusions with spliced split reads (remaining=3413)
[2026-06-08T08:43:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=2514)
[2026-06-08T08:43:21] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2491)
[2026-06-08T08:43:22] Searching for fusions with >=4 spliced events (remaining=2866)
[2026-06-08T08:43:24] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1434)
[2026-06-08T08:43:36] Filtering fusions with anchors <=23nt (remaining=1122)
[2026-06-08T08:43:37] Filtering end-to-end fusions with low support (remaining=1087)
[2026-06-08T08:43:37] Filtering fusions with no coverage around the breakpoints (remaining=1064)
[2026-06-08T08:43:38] Indexing gene sequences 
[2026-06-08T08:43:44] Filtering genes with >=30% identity (remaining=564)
[2026-06-08T08:43:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=373)
[2026-06-08T08:44:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=244)
[2026-06-08T08:44:02] Searching for additional isoforms (remaining=313)
[2026-06-08T08:44:04] Assigning confidence scores to events 
[2026-06-08T08:44:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:44:08] Writing fusions to file '1173_KTN_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:44:10] Writing discarded fusions to file '1173_KTN_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:44:45] Freeing resources
[2026-06-08T08:45:02] Done (elapsed time=00:11:34, CPU time=00:11:33, peak memory=15.8gb)