[2026-06-08T08:49:36] Launching Arriba 2.4.0
[2026-06-08T08:49:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:48] Reading chimeric alignments from 'tih_rna_sample_00644_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=12746050)
[2026-06-08T08:56:33] Marking multi-mapping alignments (marked=8527535)
[2026-06-08T08:56:38] Detecting strandedness (reverse)
[2026-06-08T08:56:38] Assigning strands to alignments 
[2026-06-08T08:56:40] Annotating alignments 
[2026-06-08T08:57:17] Filtering duplicates (remaining=7201029)
[2026-06-08T08:57:25] 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=6762238)
[2026-06-08T08:57:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6762238)
[2026-06-08T08:57:29] Filtering viral contigs with expression lower than the top 5 (remaining=6762238)
[2026-06-08T08:57:34] Filtering viral contigs with less than 5% coverage (remaining=6762238)
[2026-06-08T08:57:37] Estimating fragment length (mate gap mean=-88.7589, mate gap stddev=27.9792, read length mean=129.161)
[2026-06-08T08:57:37] Filtering read-through fragments with a distance <=10000bp (remaining=6404797)
[2026-06-08T08:57:39] Filtering inconsistently clipped mates (remaining=6292750)
[2026-06-08T08:57:42] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6126961)
[2026-06-08T08:57:46] Filtering fragments with small insert size (remaining=6126282)
[2026-06-08T08:57:48] Filtering alignments with long gaps (remaining=6126282)
[2026-06-08T08:57:51] Filtering fragments with both mates in the same gene (remaining=6125172)
[2026-06-08T08:57:53] Filtering fusions arising from hairpin structures (remaining=5781102)
[2026-06-08T08:57:56] Filtering reads with a mismatch p-value <=0.01 (remaining=2552466)
[2026-06-08T08:58:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=960559)
[2026-06-08T08:58:21] Finding fusions and counting supporting reads (total=736121)
[2026-06-08T08:58:39] Merging adjacent fusion breakpoints (remaining=726677)
[2026-06-08T08:58:40] Filtering multi-mapping fusions by alignment score and read support (remaining=427277)
[2026-06-08T08:59:17] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=425647)
[2026-06-08T08:59:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=255614)
[2026-06-08T08:59:26] Filtering fusions with <2 supporting reads (remaining=27801)
[2026-06-08T08:59:27] Filtering fusions with an e-value >=0.3 (remaining=6549)
[2026-06-08T08:59:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6597)
[2026-06-08T08:59:32] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6493)
[2026-06-08T08:59:33] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6493)
[2026-06-08T08:59:34] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6186)
[2026-06-08T08:59:40] Searching for fusions with spliced split reads (remaining=6328)
[2026-06-08T08:59:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=4088)
[2026-06-08T08:59:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4059)
[2026-06-08T08:59:47] Searching for fusions with >=4 spliced events (remaining=5108)
[2026-06-08T08:59:49] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2348)
[2026-06-08T09:00:04] Filtering fusions with anchors <=23nt (remaining=1916)
[2026-06-08T09:00:04] Filtering end-to-end fusions with low support (remaining=1816)
[2026-06-08T09:00:05] Filtering fusions with no coverage around the breakpoints (remaining=1776)
[2026-06-08T09:00:06] Indexing gene sequences 
[2026-06-08T09:00:12] Filtering genes with >=30% identity (remaining=466)
[2026-06-08T09:00:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=156)
[2026-06-08T09:00:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=142)
[2026-06-08T09:00:19] Searching for additional isoforms (remaining=183)
[2026-06-08T09:00:20] Assigning confidence scores to events 
[2026-06-08T09:00:24] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:24] Writing fusions to file 'tih_rna_sample_00644_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:00:26] Writing discarded fusions to file 'tih_rna_sample_00644_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:56] Freeing resources
[2026-06-08T09:01:14] Done (elapsed time=00:11:38, CPU time=00:11:36, peak memory=17.5gb)