[2026-06-08T08:27:29] Launching Arriba 2.4.0
[2026-06-08T08:27:29] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:27:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:42] Reading chimeric alignments from '1173_M5U_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=15988037)
[2026-06-08T08:34:36] Marking multi-mapping alignments (marked=10945968)
[2026-06-08T08:34:42] Detecting strandedness (reverse)
[2026-06-08T08:34:42] Assigning strands to alignments 
[2026-06-08T08:34:46] Annotating alignments 
[2026-06-08T08:35:35] Filtering duplicates (remaining=9108458)
[2026-06-08T08:35:45] 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=8525187)
[2026-06-08T08:35:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8525187)
[2026-06-08T08:35:51] Filtering viral contigs with expression lower than the top 5 (remaining=8525187)
[2026-06-08T08:35:58] Filtering viral contigs with less than 5% coverage (remaining=8525187)
[2026-06-08T08:36:02] Estimating fragment length (mate gap mean=-81.5883, mate gap stddev=27.0579, read length mean=121.664)
[2026-06-08T08:36:02] Filtering read-through fragments with a distance <=10000bp (remaining=8120654)
[2026-06-08T08:36:05] Filtering inconsistently clipped mates (remaining=7942931)
[2026-06-08T08:36:08] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7805956)
[2026-06-08T08:36:15] Filtering fragments with small insert size (remaining=7804159)
[2026-06-08T08:36:18] Filtering alignments with long gaps (remaining=7804159)
[2026-06-08T08:36:21] Filtering fragments with both mates in the same gene (remaining=7802864)
[2026-06-08T08:36:24] Filtering fusions arising from hairpin structures (remaining=7349068)
[2026-06-08T08:36:28] Filtering reads with a mismatch p-value <=0.01 (remaining=3331879)
[2026-06-08T08:36:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=1381463)
[2026-06-08T08:37:00] Finding fusions and counting supporting reads (total=1233254)
[2026-06-08T08:37:33] Merging adjacent fusion breakpoints (remaining=1219555)
[2026-06-08T08:37:36] Filtering multi-mapping fusions by alignment score and read support (remaining=645000)
[2026-06-08T08:38:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:38:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=643753)
[2026-06-08T08:38:41] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=462591)
[2026-06-08T08:38:43] Filtering fusions with <2 supporting reads (remaining=28025)
[2026-06-08T08:38:44] Filtering fusions with an e-value >=0.3 (remaining=5543)
[2026-06-08T08:38:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5640)
[2026-06-08T08:38:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5547)
[2026-06-08T08:38:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5547)
[2026-06-08T08:38:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5519)
[2026-06-08T08:39:10] Searching for fusions with spliced split reads (remaining=5619)
[2026-06-08T08:39:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=4029)
[2026-06-08T08:39:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3986)
[2026-06-08T08:39:23] Searching for fusions with >=4 spliced events (remaining=4694)
[2026-06-08T08:39:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2011)
[2026-06-08T08:39:44] Filtering fusions with anchors <=23nt (remaining=1519)
[2026-06-08T08:39:45] Filtering end-to-end fusions with low support (remaining=1468)
[2026-06-08T08:39:46] Filtering fusions with no coverage around the breakpoints (remaining=1430)
[2026-06-08T08:39:47] Indexing gene sequences 
[2026-06-08T08:39:54] Filtering genes with >=30% identity (remaining=474)
[2026-06-08T08:39:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=220)
[2026-06-08T08:40:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=183)
[2026-06-08T08:40:02] Searching for additional isoforms (remaining=244)
[2026-06-08T08:40:04] Assigning confidence scores to events 
[2026-06-08T08:40:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:40:09] Writing fusions to file '1173_M5U_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:40:12] Writing discarded fusions to file '1173_M5U_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:40:54] Freeing resources
[2026-06-08T08:41:20] Done (elapsed time=00:13:51, CPU time=00:13:49, peak memory=20.4gb)