[2026-06-08T08:36:27] Launching Arriba 2.4.0
[2026-06-08T08:36:27] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:36:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:36:39] Reading chimeric alignments from '1173_K7E_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=13531518)
[2026-06-08T08:43:15] Marking multi-mapping alignments (marked=9595781)
[2026-06-08T08:43:20] Detecting strandedness (reverse)
[2026-06-08T08:43:20] Assigning strands to alignments 
[2026-06-08T08:43:23] Annotating alignments 
[2026-06-08T08:44:05] Filtering duplicates (remaining=8563206)
[2026-06-08T08:44:14] 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=7694253)
[2026-06-08T08:44:16] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7694253)
[2026-06-08T08:44:18] Filtering viral contigs with expression lower than the top 5 (remaining=7694253)
[2026-06-08T08:44:24] Filtering viral contigs with less than 5% coverage (remaining=7694253)
[2026-06-08T08:44:27] Estimating fragment length (mate gap mean=-78.1366, mate gap stddev=26.9963, read length mean=114.305)
[2026-06-08T08:44:27] Filtering read-through fragments with a distance <=10000bp (remaining=7444725)
[2026-06-08T08:44:29] Filtering inconsistently clipped mates (remaining=7359032)
[2026-06-08T08:44:32] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7193450)
[2026-06-08T08:44:37] Filtering fragments with small insert size (remaining=7192153)
[2026-06-08T08:44:39] Filtering alignments with long gaps (remaining=7192153)
[2026-06-08T08:44:42] Filtering fragments with both mates in the same gene (remaining=7190519)
[2026-06-08T08:44:45] Filtering fusions arising from hairpin structures (remaining=7022857)
[2026-06-08T08:44:47] Filtering reads with a mismatch p-value <=0.01 (remaining=3015246)
[2026-06-08T08:45:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=1267037)
[2026-06-08T08:45:15] Finding fusions and counting supporting reads (total=1148511)
[2026-06-08T08:45:37] Merging adjacent fusion breakpoints (remaining=1140817)
[2026-06-08T08:45:40] Filtering multi-mapping fusions by alignment score and read support (remaining=580994)
[2026-06-08T08:46:22] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:46:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=580129)
[2026-06-08T08:46:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=496998)
[2026-06-08T08:46:35] Filtering fusions with <2 supporting reads (remaining=21295)
[2026-06-08T08:46:36] Filtering fusions with an e-value >=0.3 (remaining=3780)
[2026-06-08T08:46:37] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3813)
[2026-06-08T08:46:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3754)
[2026-06-08T08:46:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3754)
[2026-06-08T08:46:45] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3754)
[2026-06-08T08:46:52] Searching for fusions with spliced split reads (remaining=3818)
[2026-06-08T08:47:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=2882)
[2026-06-08T08:47:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2858)
[2026-06-08T08:47:03] Searching for fusions with >=4 spliced events (remaining=3353)
[2026-06-08T08:47:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1539)
[2026-06-08T08:47:18] Filtering fusions with anchors <=23nt (remaining=1168)
[2026-06-08T08:47:19] Filtering end-to-end fusions with low support (remaining=1131)
[2026-06-08T08:47:20] Filtering fusions with no coverage around the breakpoints (remaining=1101)
[2026-06-08T08:47:21] Indexing gene sequences 
[2026-06-08T08:47:26] Filtering genes with >=30% identity (remaining=360)
[2026-06-08T08:47:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=144)
[2026-06-08T08:47:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=138)
[2026-06-08T08:47:36] Searching for additional isoforms (remaining=165)
[2026-06-08T08:47:38] Assigning confidence scores to events 
[2026-06-08T08:47:43] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:43] Writing fusions to file '1173_K7E_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:47:45] Writing discarded fusions to file '1173_K7E_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:48:24] Freeing resources
[2026-06-08T08:48:45] Done (elapsed time=00:12:18, CPU time=00:12:17, peak memory=18gb)