[2026-06-08T08:23:40] Launching Arriba 2.4.0
[2026-06-08T08:23:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:23:49] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:23:53] Reading chimeric alignments from 'tih_rna_sample_00248_23H5VFLT4_s01.Aligned.sortedByCoord.out.bam' (total=12180125)
[2026-06-08T08:31:00] Marking multi-mapping alignments (marked=8174637)
[2026-06-08T08:31:05] Detecting strandedness (reverse)
[2026-06-08T08:31:05] Assigning strands to alignments 
[2026-06-08T08:31:08] Annotating alignments 
[2026-06-08T08:31:52] Filtering duplicates (remaining=7671439)
[2026-06-08T08:31:59] 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=7171934)
[2026-06-08T08:32:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7171934)
[2026-06-08T08:32:04] Filtering viral contigs with expression lower than the top 5 (remaining=7171934)
[2026-06-08T08:32:09] Filtering viral contigs with less than 5% coverage (remaining=7171934)
[2026-06-08T08:32:12] Estimating fragment length (mate gap mean=-86.1289, mate gap stddev=28.9773, read length mean=126.651)
[2026-06-08T08:32:12] Filtering read-through fragments with a distance <=10000bp (remaining=6677490)
[2026-06-08T08:32:14] Filtering inconsistently clipped mates (remaining=6535468)
[2026-06-08T08:32:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6003103)
[2026-06-08T08:32:22] Filtering fragments with small insert size (remaining=6001619)
[2026-06-08T08:32:24] Filtering alignments with long gaps (remaining=6001619)
[2026-06-08T08:32:27] Filtering fragments with both mates in the same gene (remaining=5999991)
[2026-06-08T08:32:30] Filtering fusions arising from hairpin structures (remaining=5457822)
[2026-06-08T08:32:33] Filtering reads with a mismatch p-value <=0.01 (remaining=2175632)
[2026-06-08T08:32:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=1483338)
[2026-06-08T08:32:59] Finding fusions and counting supporting reads (total=1193475)
[2026-06-08T08:33:20] Merging adjacent fusion breakpoints (remaining=1180628)
[2026-06-08T08:33:22] Filtering multi-mapping fusions by alignment score and read support (remaining=667924)
[2026-06-08T08:34:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:34:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=665611)
[2026-06-08T08:34:11] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=433550)
[2026-06-08T08:34:13] Filtering fusions with <2 supporting reads (remaining=38042)
[2026-06-08T08:34:14] Filtering fusions with an e-value >=0.3 (remaining=7225)
[2026-06-08T08:34:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7278)
[2026-06-08T08:34:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7045)
[2026-06-08T08:34:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7045)
[2026-06-08T08:34:22] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6815)
[2026-06-08T08:34:29] Searching for fusions with spliced split reads (remaining=6828)
[2026-06-08T08:34:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=4453)
[2026-06-08T08:34:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4414)
[2026-06-08T08:34:38] Searching for fusions with >=4 spliced events (remaining=5674)
[2026-06-08T08:34:40] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2316)
[2026-06-08T08:34:54] Filtering fusions with anchors <=23nt (remaining=1946)
[2026-06-08T08:34:55] Filtering end-to-end fusions with low support (remaining=1902)
[2026-06-08T08:34:56] Filtering fusions with no coverage around the breakpoints (remaining=1880)
[2026-06-08T08:34:57] Indexing gene sequences 
[2026-06-08T08:35:03] Filtering genes with >=30% identity (remaining=607)
[2026-06-08T08:35:06] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=273)
[2026-06-08T08:35:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=203)
[2026-06-08T08:35:11] Searching for additional isoforms (remaining=280)
[2026-06-08T08:35:13] Assigning confidence scores to events 
[2026-06-08T08:35:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:35:18] Writing fusions to file 'tih_rna_sample_00248_23H5VFLT4_s01.arriba.fusions.tsv' 
[2026-06-08T08:35:21] Writing discarded fusions to file 'tih_rna_sample_00248_23H5VFLT4_s01.arriba.fusions.discarded.tsv'
[2026-06-08T08:35:58] Freeing resources
[2026-06-08T08:36:19] Done (elapsed time=00:12:39, CPU time=00:12:38, peak memory=17.8gb)