[2026-06-08T08:35:10] Launching Arriba 2.4.0
[2026-06-08T08:35:10] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:22] Reading chimeric alignments from 'tih_rna_sample_00150_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=8225022)
[2026-06-08T08:41:00] Marking multi-mapping alignments (marked=5022101)
[2026-06-08T08:41:03] Detecting strandedness (reverse)
[2026-06-08T08:41:03] Assigning strands to alignments 
[2026-06-08T08:41:05] Annotating alignments 
[2026-06-08T08:41:33] Filtering duplicates (remaining=4152333)
[2026-06-08T08:41:38] 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=4009582)
[2026-06-08T08:41:39] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4009582)
[2026-06-08T08:41:41] Filtering viral contigs with expression lower than the top 5 (remaining=4009582)
[2026-06-08T08:41:45] Filtering viral contigs with less than 5% coverage (remaining=4009582)
[2026-06-08T08:41:47] Estimating fragment length (mate gap mean=-86.4109, mate gap stddev=28.3377, read length mean=132.94)
[2026-06-08T08:41:47] Filtering read-through fragments with a distance <=10000bp (remaining=3747977)
[2026-06-08T08:41:49] Filtering inconsistently clipped mates (remaining=3693843)
[2026-06-08T08:41:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3604472)
[2026-06-08T08:41:53] Filtering fragments with small insert size (remaining=3603994)
[2026-06-08T08:41:55] Filtering alignments with long gaps (remaining=3603994)
[2026-06-08T08:41:57] Filtering fragments with both mates in the same gene (remaining=3603292)
[2026-06-08T08:41:58] Filtering fusions arising from hairpin structures (remaining=3434909)
[2026-06-08T08:42:00] Filtering reads with a mismatch p-value <=0.01 (remaining=1539675)
[2026-06-08T08:42:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=680808)
[2026-06-08T08:42:17] Finding fusions and counting supporting reads (total=529895)
[2026-06-08T08:42:30] Merging adjacent fusion breakpoints (remaining=525518)
[2026-06-08T08:42:31] Filtering multi-mapping fusions by alignment score and read support (remaining=342090)
[2026-06-08T08:42:58] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:43:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=340713)
[2026-06-08T08:43:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=173395)
[2026-06-08T08:43:04] Filtering fusions with <2 supporting reads (remaining=24029)
[2026-06-08T08:43:04] Filtering fusions with an e-value >=0.3 (remaining=6273)
[2026-06-08T08:43:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6307)
[2026-06-08T08:43:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6267)
[2026-06-08T08:43:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6267)
[2026-06-08T08:43:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5571)
[2026-06-08T08:43:13] Searching for fusions with spliced split reads (remaining=5644)
[2026-06-08T08:43:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=3683)
[2026-06-08T08:43:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3638)
[2026-06-08T08:43:18] Searching for fusions with >=4 spliced events (remaining=4213)
[2026-06-08T08:43:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1357)
[2026-06-08T08:43:31] Filtering fusions with anchors <=23nt (remaining=1120)
[2026-06-08T08:43:32] Filtering end-to-end fusions with low support (remaining=1081)
[2026-06-08T08:43:32] Filtering fusions with no coverage around the breakpoints (remaining=1050)
[2026-06-08T08:43:33] Indexing gene sequences 
[2026-06-08T08:43:37] Filtering genes with >=30% identity (remaining=341)
[2026-06-08T08:43:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=139)
[2026-06-08T08:43:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=133)
[2026-06-08T08:43:41] Searching for additional isoforms (remaining=157)
[2026-06-08T08:43:42] Assigning confidence scores to events 
[2026-06-08T08:43:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:43:44] Writing fusions to file 'tih_rna_sample_00150_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:43:46] Writing discarded fusions to file 'tih_rna_sample_00150_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:44:06] Freeing resources
[2026-06-08T08:44:20] Done (elapsed time=00:09:10, CPU time=00:09:09, peak memory=12.6gb)