[2026-06-08T08:39:40] Launching Arriba 2.4.0
[2026-06-08T08:39:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:55] Reading chimeric alignments from 'tih_rna_sample_00763_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11207649)
[2026-06-08T08:48:12] Marking multi-mapping alignments (marked=7128581)
[2026-06-08T08:48:19] Detecting strandedness (reverse)
[2026-06-08T08:48:19] Assigning strands to alignments 
[2026-06-08T08:48:23] Annotating alignments 
[2026-06-08T08:49:24] Filtering duplicates (remaining=7048732)
[2026-06-08T08:49:42] 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=6804674)
[2026-06-08T08:49:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6804674)
[2026-06-08T08:49:49] Filtering viral contigs with expression lower than the top 5 (remaining=6804674)
[2026-06-08T08:49:58] Filtering viral contigs with less than 5% coverage (remaining=6804674)
[2026-06-08T08:50:02] Estimating fragment length (mate gap mean=-86.1459, mate gap stddev=27.5037, read length mean=128.681)
[2026-06-08T08:50:02] Filtering read-through fragments with a distance <=10000bp (remaining=6302841)
[2026-06-08T08:50:06] Filtering inconsistently clipped mates (remaining=6198372)
[2026-06-08T08:50:09] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6080954)
[2026-06-08T08:50:17] Filtering fragments with small insert size (remaining=6080088)
[2026-06-08T08:50:21] Filtering alignments with long gaps (remaining=6080088)
[2026-06-08T08:50:25] Filtering fragments with both mates in the same gene (remaining=6078938)
[2026-06-08T08:50:28] Filtering fusions arising from hairpin structures (remaining=5769958)
[2026-06-08T08:50:33] Filtering reads with a mismatch p-value <=0.01 (remaining=2836030)
[2026-06-08T08:50:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=1200828)
[2026-06-08T08:51:06] Finding fusions and counting supporting reads (total=862968)
[2026-06-08T08:51:35] Merging adjacent fusion breakpoints (remaining=852207)
[2026-06-08T08:51:38] Filtering multi-mapping fusions by alignment score and read support (remaining=509758)
[2026-06-08T08:52:35] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:52:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=508182)
[2026-06-08T08:52:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=298309)
[2026-06-08T08:52:53] Filtering fusions with <2 supporting reads (remaining=38554)
[2026-06-08T08:52:55] Filtering fusions with an e-value >=0.3 (remaining=9185)
[2026-06-08T08:52:56] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9230)
[2026-06-08T08:53:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9090)
[2026-06-08T08:53:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9090)
[2026-06-08T08:53:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8484)
[2026-06-08T08:53:16] Searching for fusions with spliced split reads (remaining=8597)
[2026-06-08T08:53:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=5182)
[2026-06-08T08:53:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5126)
[2026-06-08T08:53:32] Searching for fusions with >=4 spliced events (remaining=6262)
[2026-06-08T08:53:34] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2662)
[2026-06-08T08:54:03] Filtering fusions with anchors <=23nt (remaining=2255)
[2026-06-08T08:54:04] Filtering end-to-end fusions with low support (remaining=2194)
[2026-06-08T08:54:06] Filtering fusions with no coverage around the breakpoints (remaining=2144)
[2026-06-08T08:54:07] Indexing gene sequences 
[2026-06-08T08:54:23] Filtering genes with >=30% identity (remaining=610)
[2026-06-08T08:54:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=231)
[2026-06-08T08:54:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=208)
[2026-06-08T08:54:40] Searching for additional isoforms (remaining=264)
[2026-06-08T08:54:43] Assigning confidence scores to events 
[2026-06-08T08:54:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:54:52] Writing fusions to file 'tih_rna_sample_00763_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:54:56] Writing discarded fusions to file 'tih_rna_sample_00763_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:56:04] Freeing resources
[2026-06-08T08:56:52] Done (elapsed time=00:17:12, CPU time=00:17:10, peak memory=15.8gb)