[2026-06-08T08:15:18] Launching Arriba 2.4.0
[2026-06-08T08:15:18] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:15:32] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:15:36] Reading chimeric alignments from '1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=9376978)
[2026-06-08T08:21:30] Marking multi-mapping alignments (marked=6614623)
[2026-06-08T08:21:33] Detecting strandedness (reverse)
[2026-06-08T08:21:33] Assigning strands to alignments 
[2026-06-08T08:21:35] Annotating alignments 
[2026-06-08T08:22:06] Filtering duplicates (remaining=6222688)
[2026-06-08T08:22:13] 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=5632604)
[2026-06-08T08:22:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5632604)
[2026-06-08T08:22:16] Filtering viral contigs with expression lower than the top 5 (remaining=5632604)
[2026-06-08T08:22:21] Filtering viral contigs with less than 5% coverage (remaining=5632604)
[2026-06-08T08:22:23] Estimating fragment length (mate gap mean=-76.8999, mate gap stddev=28.1511, read length mean=112.405)
[2026-06-08T08:22:23] Filtering read-through fragments with a distance <=10000bp (remaining=5450017)
[2026-06-08T08:22:25] Filtering inconsistently clipped mates (remaining=5399111)
[2026-06-08T08:22:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5275126)
[2026-06-08T08:22:30] Filtering fragments with small insert size (remaining=5274123)
[2026-06-08T08:22:32] Filtering alignments with long gaps (remaining=5274122)
[2026-06-08T08:22:34] Filtering fragments with both mates in the same gene (remaining=5273043)
[2026-06-08T08:22:36] Filtering fusions arising from hairpin structures (remaining=5169204)
[2026-06-08T08:22:38] Filtering reads with a mismatch p-value <=0.01 (remaining=2198273)
[2026-06-08T08:22:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=749471)
[2026-06-08T08:22:58] Finding fusions and counting supporting reads (total=652074)
[2026-06-08T08:23:14] Merging adjacent fusion breakpoints (remaining=648626)
[2026-06-08T08:23:16] Filtering multi-mapping fusions by alignment score and read support (remaining=343353)
[2026-06-08T08:23:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:23:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=342649)
[2026-06-08T08:23:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=291931)
[2026-06-08T08:23:54] Filtering fusions with <2 supporting reads (remaining=16632)
[2026-06-08T08:23:55] Filtering fusions with an e-value >=0.3 (remaining=3480)
[2026-06-08T08:23:56] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3521)
[2026-06-08T08:23:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3480)
[2026-06-08T08:24:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3480)
[2026-06-08T08:24:02] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3464)
[2026-06-08T08:24:07] Searching for fusions with spliced split reads (remaining=3528)
[2026-06-08T08:24:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=2668)
[2026-06-08T08:24:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2633)
[2026-06-08T08:24:14] Searching for fusions with >=4 spliced events (remaining=2904)
[2026-06-08T08:24:15] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1156)
[2026-06-08T08:24:33] Filtering fusions with anchors <=23nt (remaining=859)
[2026-06-08T08:24:34] Filtering end-to-end fusions with low support (remaining=828)
[2026-06-08T08:24:34] Filtering fusions with no coverage around the breakpoints (remaining=804)
[2026-06-08T08:24:35] Indexing gene sequences 
[2026-06-08T08:24:40] Filtering genes with >=30% identity (remaining=266)
[2026-06-08T08:24:42] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=135)
[2026-06-08T08:24:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=129)
[2026-06-08T08:24:48] Searching for additional isoforms (remaining=149)
[2026-06-08T08:24:50] Assigning confidence scores to events 
[2026-06-08T08:24:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:24:54] Writing fusions to file '1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:24:55] Writing discarded fusions to file '1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:25:30] Freeing resources
[2026-06-08T08:25:46] Done (elapsed time=00:10:28, CPU time=00:10:27, peak memory=13.7gb)