[2026-06-08T08:29:31] Launching Arriba 2.4.0
[2026-06-08T08:29:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:29:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:29:50] Reading chimeric alignments from '1173_9C_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=17166339)
[2026-06-08T08:38:41] Marking multi-mapping alignments (marked=11908923)
[2026-06-08T08:38:48] Detecting strandedness (no)
[2026-06-08T08:38:48] Annotating alignments 
[2026-06-08T08:39:50] Filtering duplicates (remaining=11558812)
[2026-06-08T08:40:02] 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=10175180)
[2026-06-08T08:40:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=10175180)
[2026-06-08T08:40:08] Filtering viral contigs with expression lower than the top 5 (remaining=10175180)
[2026-06-08T08:40:15] Filtering viral contigs with less than 5% coverage (remaining=10175180)
[2026-06-08T08:40:18] Estimating fragment length (mate gap mean=-81.4918, mate gap stddev=26.9305, read length mean=122.521)
[2026-06-08T08:40:19] Filtering read-through fragments with a distance <=10000bp (remaining=9859393)
[2026-06-08T08:40:22] Filtering inconsistently clipped mates (remaining=9680552)
[2026-06-08T08:40:28] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9510949)
[2026-06-08T08:40:44] Filtering fragments with small insert size (remaining=9509337)
[2026-06-08T08:40:50] Filtering alignments with long gaps (remaining=9509336)
[2026-06-08T08:40:56] Filtering fragments with both mates in the same gene (remaining=9507665)
[2026-06-08T08:41:03] Filtering fusions arising from hairpin structures (remaining=9018632)
[2026-06-08T08:41:07] Filtering reads with a mismatch p-value <=0.01 (remaining=4564160)
[2026-06-08T08:41:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=2360538)
[2026-06-08T08:41:56] Finding fusions and counting supporting reads (total=2229382)
[2026-06-08T08:42:26] Merging adjacent fusion breakpoints (remaining=2217763)
[2026-06-08T08:42:29] Filtering multi-mapping fusions by alignment score and read support (remaining=1168777)
[2026-06-08T08:43:24] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:43:38] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1167557)
[2026-06-08T08:43:40] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1004470)
[2026-06-08T08:43:41] Filtering fusions with <2 supporting reads (remaining=26178)
[2026-06-08T08:43:43] Filtering fusions with an e-value >=0.3 (remaining=4113)
[2026-06-08T08:43:44] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4232)
[2026-06-08T08:43:51] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4163)
[2026-06-08T08:43:52] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4163)
[2026-06-08T08:43:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4134)
[2026-06-08T08:44:05] Searching for fusions with spliced split reads (remaining=4176)
[2026-06-08T08:44:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=3022)
[2026-06-08T08:44:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2982)
[2026-06-08T08:44:19] Searching for fusions with >=4 spliced events (remaining=3598)
[2026-06-08T08:44:21] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1573)
[2026-06-08T08:44:39] Filtering fusions with anchors <=23nt (remaining=1284)
[2026-06-08T08:44:41] Filtering end-to-end fusions with low support (remaining=1254)
[2026-06-08T08:44:42] Filtering fusions with no coverage around the breakpoints (remaining=1237)
[2026-06-08T08:44:43] Indexing gene sequences 
[2026-06-08T08:44:50] Filtering genes with >=30% identity (remaining=496)
[2026-06-08T08:44:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=317)
[2026-06-08T08:45:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=265)
[2026-06-08T08:45:02] Searching for additional isoforms (remaining=349)
[2026-06-08T08:45:05] Assigning confidence scores to events 
[2026-06-08T08:45:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:45:12] Writing fusions to file '1173_9C_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:45:15] Writing discarded fusions to file '1173_9C_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:46:11] Freeing resources
[2026-06-08T08:46:40] Done (elapsed time=00:17:09, CPU time=00:17:08, peak memory=22.2gb)