[2026-06-08T08:17:06] Launching Arriba 2.4.0
[2026-06-08T08:17:06] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:17:19] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:17:23] Reading chimeric alignments from 'tih_rna_sample_00089_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=6245343)
[2026-06-08T08:22:15] Marking multi-mapping alignments (marked=4021210)
[2026-06-08T08:22:18] Detecting strandedness (reverse)
[2026-06-08T08:22:18] Assigning strands to alignments 
[2026-06-08T08:22:19] Annotating alignments 
[2026-06-08T08:22:40] Filtering duplicates (remaining=3392757)
[2026-06-08T08:22:44] 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=3229134)
[2026-06-08T08:22:46] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3229134)
[2026-06-08T08:22:47] Filtering viral contigs with expression lower than the top 5 (remaining=3229134)
[2026-06-08T08:22:50] Filtering viral contigs with less than 5% coverage (remaining=3229134)
[2026-06-08T08:22:51] Estimating fragment length (mate gap mean=-87.1969, mate gap stddev=28.5532, read length mean=134.197)
[2026-06-08T08:22:52] Filtering read-through fragments with a distance <=10000bp (remaining=3008576)
[2026-06-08T08:22:53] Filtering inconsistently clipped mates (remaining=2956733)
[2026-06-08T08:22:54] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2873156)
[2026-06-08T08:22:57] Filtering fragments with small insert size (remaining=2872679)
[2026-06-08T08:22:58] Filtering alignments with long gaps (remaining=2872678)
[2026-06-08T08:22:59] Filtering fragments with both mates in the same gene (remaining=2872141)
[2026-06-08T08:23:01] Filtering fusions arising from hairpin structures (remaining=2702039)
[2026-06-08T08:23:02] Filtering reads with a mismatch p-value <=0.01 (remaining=1214139)
[2026-06-08T08:23:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=530588)
[2026-06-08T08:23:16] Finding fusions and counting supporting reads (total=440056)
[2026-06-08T08:23:26] Merging adjacent fusion breakpoints (remaining=435561)
[2026-06-08T08:23:27] Filtering multi-mapping fusions by alignment score and read support (remaining=270102)
[2026-06-08T08:23:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:23:51] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=268419)
[2026-06-08T08:23:52] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=137217)
[2026-06-08T08:23:52] Filtering fusions with <2 supporting reads (remaining=18167)
[2026-06-08T08:23:53] Filtering fusions with an e-value >=0.3 (remaining=6322)
[2026-06-08T08:23:53] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6364)
[2026-06-08T08:23:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6311)
[2026-06-08T08:23:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6312)
[2026-06-08T08:23:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3960)
[2026-06-08T08:23:59] Searching for fusions with spliced split reads (remaining=4012)
[2026-06-08T08:24:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=2752)
[2026-06-08T08:24:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2726)
[2026-06-08T08:24:03] Searching for fusions with >=4 spliced events (remaining=3027)
[2026-06-08T08:24:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1039)
[2026-06-08T08:24:20] Filtering fusions with anchors <=23nt (remaining=822)
[2026-06-08T08:24:20] Filtering end-to-end fusions with low support (remaining=795)
[2026-06-08T08:24:20] Filtering fusions with no coverage around the breakpoints (remaining=767)
[2026-06-08T08:24:21] Indexing gene sequences 
[2026-06-08T08:24:25] Filtering genes with >=30% identity (remaining=293)
[2026-06-08T08:24:26] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=173)
[2026-06-08T08:24:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=149)
[2026-06-08T08:24:29] Searching for additional isoforms (remaining=188)
[2026-06-08T08:24:30] Assigning confidence scores to events 
[2026-06-08T08:24:31] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:24:32] Writing fusions to file 'tih_rna_sample_00089_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:24:33] Writing discarded fusions to file 'tih_rna_sample_00089_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:24:51] Freeing resources
[2026-06-08T08:25:02] Done (elapsed time=00:07:56, CPU time=00:07:55, peak memory=10.7gb)