[2026-06-08T08:34:30] Launching Arriba 2.4.0
[2026-06-08T08:34:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:34:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:34:43] Reading chimeric alignments from '1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=17157925)
[2026-06-08T08:41:51] Marking multi-mapping alignments (marked=12267221)
[2026-06-08T08:41:58] Detecting strandedness (reverse)
[2026-06-08T08:41:58] Assigning strands to alignments 
[2026-06-08T08:42:01] Annotating alignments 
[2026-06-08T08:42:56] Filtering duplicates (remaining=9483916)
[2026-06-08T08:43:07] 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=8295593)
[2026-06-08T08:43:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8295593)
[2026-06-08T08:43:14] Filtering viral contigs with expression lower than the top 5 (remaining=8295593)
[2026-06-08T08:43:21] Filtering viral contigs with less than 5% coverage (remaining=8295593)
[2026-06-08T08:43:25] Estimating fragment length (mate gap mean=-76.7476, mate gap stddev=27.0367, read length mean=114.686)
[2026-06-08T08:43:25] Filtering read-through fragments with a distance <=10000bp (remaining=8003178)
[2026-06-08T08:43:28] Filtering inconsistently clipped mates (remaining=7870262)
[2026-06-08T08:43:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7698506)
[2026-06-08T08:43:37] Filtering fragments with small insert size (remaining=7696077)
[2026-06-08T08:43:41] Filtering alignments with long gaps (remaining=7696076)
[2026-06-08T08:43:44] Filtering fragments with both mates in the same gene (remaining=7694228)
[2026-06-08T08:43:47] Filtering fusions arising from hairpin structures (remaining=7409321)
[2026-06-08T08:43:51] Filtering reads with a mismatch p-value <=0.01 (remaining=2990744)
[2026-06-08T08:44:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=1207326)
[2026-06-08T08:44:22] Finding fusions and counting supporting reads (total=1146797)
[2026-06-08T08:44:50] Merging adjacent fusion breakpoints (remaining=1137916)
[2026-06-08T08:44:53] Filtering multi-mapping fusions by alignment score and read support (remaining=535423)
[2026-06-08T08:45:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:45:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=534215)
[2026-06-08T08:45:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=420487)
[2026-06-08T08:46:01] Filtering fusions with <2 supporting reads (remaining=17298)
[2026-06-08T08:46:02] Filtering fusions with an e-value >=0.3 (remaining=3580)
[2026-06-08T08:46:04] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3658)
[2026-06-08T08:46:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3587)
[2026-06-08T08:46:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3587)
[2026-06-08T08:46:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3586)
[2026-06-08T08:46:23] Searching for fusions with spliced split reads (remaining=3627)
[2026-06-08T08:46:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=2720)
[2026-06-08T08:46:34] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2701)
[2026-06-08T08:46:35] Searching for fusions with >=4 spliced events (remaining=3030)
[2026-06-08T08:46:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1464)
[2026-06-08T08:46:57] Filtering fusions with anchors <=23nt (remaining=959)
[2026-06-08T08:46:58] Filtering end-to-end fusions with low support (remaining=919)
[2026-06-08T08:46:59] Filtering fusions with no coverage around the breakpoints (remaining=873)
[2026-06-08T08:47:01] Indexing gene sequences 
[2026-06-08T08:47:05] Filtering genes with >=30% identity (remaining=319)
[2026-06-08T08:47:07] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=128)
[2026-06-08T08:47:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=120)
[2026-06-08T08:47:13] Searching for additional isoforms (remaining=133)
[2026-06-08T08:47:15] Assigning confidence scores to events 
[2026-06-08T08:47:20] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:20] Writing fusions to file '1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:47:22] Writing discarded fusions to file '1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:48:06] Freeing resources
[2026-06-08T08:48:32] Done (elapsed time=00:14:02, CPU time=00:14:01, peak memory=21.6gb)