[2026-06-08T08:36:33] Launching Arriba 2.4.0
[2026-06-08T08:36:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:36:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:36:48] Reading chimeric alignments from '1173_HOB_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=15825738)
[2026-06-08T08:43:43] Marking multi-mapping alignments (marked=11123854)
[2026-06-08T08:43:49] Detecting strandedness (reverse)
[2026-06-08T08:43:49] Assigning strands to alignments 
[2026-06-08T08:43:51] Annotating alignments 
[2026-06-08T08:44:35] Filtering duplicates (remaining=11424277)
[2026-06-08T08:44:46] 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=9926755)
[2026-06-08T08:44:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9926755)
[2026-06-08T08:44:51] Filtering viral contigs with expression lower than the top 5 (remaining=9926755)
[2026-06-08T08:44:58] Filtering viral contigs with less than 5% coverage (remaining=9926755)
[2026-06-08T08:45:01] Estimating fragment length (mate gap mean=-80.2379, mate gap stddev=26.8427, read length mean=120.597)
[2026-06-08T08:45:01] Filtering read-through fragments with a distance <=10000bp (remaining=9565235)
[2026-06-08T08:45:04] Filtering inconsistently clipped mates (remaining=9436541)
[2026-06-08T08:45:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9223375)
[2026-06-08T08:45:13] Filtering fragments with small insert size (remaining=9222055)
[2026-06-08T08:45:16] Filtering alignments with long gaps (remaining=9222055)
[2026-06-08T08:45:19] Filtering fragments with both mates in the same gene (remaining=9220142)
[2026-06-08T08:45:22] Filtering fusions arising from hairpin structures (remaining=8899017)
[2026-06-08T08:45:25] Filtering reads with a mismatch p-value <=0.01 (remaining=4349937)
[2026-06-08T08:45:44] Filtering reads with low entropy (k-mer content >=60%) (remaining=2166982)
[2026-06-08T08:46:00] Finding fusions and counting supporting reads (total=2023106)
[2026-06-08T08:46:25] Merging adjacent fusion breakpoints (remaining=2011906)
[2026-06-08T08:46:29] Filtering multi-mapping fusions by alignment score and read support (remaining=972000)
[2026-06-08T08:47:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:47:23] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=970841)
[2026-06-08T08:47:24] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=833688)
[2026-06-08T08:47:26] Filtering fusions with <2 supporting reads (remaining=26231)
[2026-06-08T08:47:27] Filtering fusions with an e-value >=0.3 (remaining=3992)
[2026-06-08T08:47:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4072)
[2026-06-08T08:47:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4015)
[2026-06-08T08:47:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4022)
[2026-06-08T08:47:38] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3963)
[2026-06-08T08:47:47] Searching for fusions with spliced split reads (remaining=4065)
[2026-06-08T08:47:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=2981)
[2026-06-08T08:47:57] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2961)
[2026-06-08T08:47:58] Searching for fusions with >=4 spliced events (remaining=3547)
[2026-06-08T08:48:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1515)
[2026-06-08T08:48:15] Filtering fusions with anchors <=23nt (remaining=1153)
[2026-06-08T08:48:16] Filtering end-to-end fusions with low support (remaining=1127)
[2026-06-08T08:48:17] Filtering fusions with no coverage around the breakpoints (remaining=1100)
[2026-06-08T08:48:19] Indexing gene sequences 
[2026-06-08T08:48:24] Filtering genes with >=30% identity (remaining=343)
[2026-06-08T08:48:26] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=148)
[2026-06-08T08:48:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=141)
[2026-06-08T08:48:31] Searching for additional isoforms (remaining=174)
[2026-06-08T08:48:33] Assigning confidence scores to events 
[2026-06-08T08:48:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:48:39] Writing fusions to file '1173_HOB_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:48:41] Writing discarded fusions to file '1173_HOB_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:49:28] Freeing resources
[2026-06-08T08:49:52] Done (elapsed time=00:13:19, CPU time=00:13:18, peak memory=20.9gb)