[2026-06-08T08:35:30] Launching Arriba 2.4.0
[2026-06-08T08:35:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:44] Reading chimeric alignments from 'tih_rna_sample_00639_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=13375520)
[2026-06-08T08:43:20] Marking multi-mapping alignments (marked=8849914)
[2026-06-08T08:43:28] Detecting strandedness (reverse)
[2026-06-08T08:43:28] Assigning strands to alignments 
[2026-06-08T08:43:32] Annotating alignments 
[2026-06-08T08:44:40] Filtering duplicates (remaining=5967105)
[2026-06-08T08:44:51] 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=5622718)
[2026-06-08T08:44:55] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5622718)
[2026-06-08T08:44:59] Filtering viral contigs with expression lower than the top 5 (remaining=5622718)
[2026-06-08T08:45:07] Filtering viral contigs with less than 5% coverage (remaining=5622718)
[2026-06-08T08:45:12] Estimating fragment length (mate gap mean=-84.3041, mate gap stddev=27.1902, read length mean=120.715)
[2026-06-08T08:45:12] Filtering read-through fragments with a distance <=10000bp (remaining=5269836)
[2026-06-08T08:45:16] Filtering inconsistently clipped mates (remaining=5183602)
[2026-06-08T08:45:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5076068)
[2026-06-08T08:45:27] Filtering fragments with small insert size (remaining=5074998)
[2026-06-08T08:45:30] Filtering alignments with long gaps (remaining=5074998)
[2026-06-08T08:45:34] Filtering fragments with both mates in the same gene (remaining=5074069)
[2026-06-08T08:45:39] Filtering fusions arising from hairpin structures (remaining=4844349)
[2026-06-08T08:45:43] Filtering reads with a mismatch p-value <=0.01 (remaining=1947971)
[2026-06-08T08:45:58] Filtering reads with low entropy (k-mer content >=60%) (remaining=735115)
[2026-06-08T08:46:11] Finding fusions and counting supporting reads (total=592406)
[2026-06-08T08:46:44] Merging adjacent fusion breakpoints (remaining=583220)
[2026-06-08T08:46:47] Filtering multi-mapping fusions by alignment score and read support (remaining=347259)
[2026-06-08T08:47:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:48:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=346339)
[2026-06-08T08:48:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=205642)
[2026-06-08T08:48:11] Filtering fusions with <2 supporting reads (remaining=26092)
[2026-06-08T08:48:13] Filtering fusions with an e-value >=0.3 (remaining=5642)
[2026-06-08T08:48:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5672)
[2026-06-08T08:48:20] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5581)
[2026-06-08T08:48:21] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5581)
[2026-06-08T08:48:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5452)
[2026-06-08T08:48:32] Searching for fusions with spliced split reads (remaining=5558)
[2026-06-08T08:48:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=3432)
[2026-06-08T08:48:43] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3414)
[2026-06-08T08:48:44] Searching for fusions with >=4 spliced events (remaining=4320)
[2026-06-08T08:48:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2147)
[2026-06-08T08:49:10] Filtering fusions with anchors <=23nt (remaining=1769)
[2026-06-08T08:49:12] Filtering end-to-end fusions with low support (remaining=1715)
[2026-06-08T08:49:13] Filtering fusions with no coverage around the breakpoints (remaining=1679)
[2026-06-08T08:49:14] Indexing gene sequences 
[2026-06-08T08:49:24] Filtering genes with >=30% identity (remaining=488)
[2026-06-08T08:49:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=153)
[2026-06-08T08:49:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=128)
[2026-06-08T08:49:35] Searching for additional isoforms (remaining=191)
[2026-06-08T08:49:37] Assigning confidence scores to events 
[2026-06-08T08:49:42] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:49:42] Writing fusions to file 'tih_rna_sample_00639_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:49:44] Writing discarded fusions to file 'tih_rna_sample_00639_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:41] Freeing resources
[2026-06-08T08:51:23] Done (elapsed time=00:15:53, CPU time=00:15:52, peak memory=17.8gb)