[2026-06-08T08:40:36] Launching Arriba 2.4.0
[2026-06-08T08:40:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:40:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:48] Reading chimeric alignments from 'tih_rna_sample_00758_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11014895)
[2026-06-08T08:47:24] Marking multi-mapping alignments (marked=6899585)
[2026-06-08T08:47:28] Detecting strandedness (reverse)
[2026-06-08T08:47:28] Assigning strands to alignments 
[2026-06-08T08:47:30] Annotating alignments 
[2026-06-08T08:48:03] Filtering duplicates (remaining=6969452)
[2026-06-08T08:48:10] 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=6671024)
[2026-06-08T08:48:12] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6671024)
[2026-06-08T08:48:14] Filtering viral contigs with expression lower than the top 5 (remaining=6671024)
[2026-06-08T08:48:19] Filtering viral contigs with less than 5% coverage (remaining=6671024)
[2026-06-08T08:48:22] Estimating fragment length (mate gap mean=-88.2371, mate gap stddev=29.5872, read length mean=135.986)
[2026-06-08T08:48:22] Filtering read-through fragments with a distance <=10000bp (remaining=6319482)
[2026-06-08T08:48:24] Filtering inconsistently clipped mates (remaining=6220147)
[2026-06-08T08:48:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6090854)
[2026-06-08T08:48:30] Filtering fragments with small insert size (remaining=6090212)
[2026-06-08T08:48:32] Filtering alignments with long gaps (remaining=6090212)
[2026-06-08T08:48:34] Filtering fragments with both mates in the same gene (remaining=6089088)
[2026-06-08T08:48:36] Filtering fusions arising from hairpin structures (remaining=5729768)
[2026-06-08T08:48:39] Filtering reads with a mismatch p-value <=0.01 (remaining=2890459)
[2026-06-08T08:48:52] Filtering reads with low entropy (k-mer content >=60%) (remaining=960562)
[2026-06-08T08:49:02] Finding fusions and counting supporting reads (total=694912)
[2026-06-08T08:49:17] Merging adjacent fusion breakpoints (remaining=689201)
[2026-06-08T08:49:18] Filtering multi-mapping fusions by alignment score and read support (remaining=435250)
[2026-06-08T08:49:50] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:57] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=432462)
[2026-06-08T08:49:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=251699)
[2026-06-08T08:49:59] Filtering fusions with <2 supporting reads (remaining=36836)
[2026-06-08T08:49:59] Filtering fusions with an e-value >=0.3 (remaining=11403)
[2026-06-08T08:50:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11473)
[2026-06-08T08:50:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11356)
[2026-06-08T08:50:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11356)
[2026-06-08T08:50:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8334)
[2026-06-08T08:50:11] Searching for fusions with spliced split reads (remaining=8348)
[2026-06-08T08:50:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=5043)
[2026-06-08T08:50:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4972)
[2026-06-08T08:50:18] Searching for fusions with >=4 spliced events (remaining=5853)
[2026-06-08T08:50:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2035)
[2026-06-08T08:50:34] Filtering fusions with anchors <=23nt (remaining=1603)
[2026-06-08T08:50:35] Filtering end-to-end fusions with low support (remaining=1557)
[2026-06-08T08:50:35] Filtering fusions with no coverage around the breakpoints (remaining=1516)
[2026-06-08T08:50:36] Indexing gene sequences 
[2026-06-08T08:50:41] Filtering genes with >=30% identity (remaining=414)
[2026-06-08T08:50:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=182)
[2026-06-08T08:50:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=177)
[2026-06-08T08:50:50] Searching for additional isoforms (remaining=223)
[2026-06-08T08:50:51] Assigning confidence scores to events 
[2026-06-08T08:50:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:50:55] Writing fusions to file 'tih_rna_sample_00758_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:50:57] Writing discarded fusions to file 'tih_rna_sample_00758_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:51:23] Freeing resources
[2026-06-08T08:51:40] Done (elapsed time=00:11:04, CPU time=00:11:03, peak memory=15.5gb)