[2026-06-08T07:56:16] Launching Arriba 2.4.0
[2026-06-08T07:56:16] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:56:33] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:56:39] Reading chimeric alignments from 'tih_rna_sample_00111_23H5VFLT4_s30.Aligned.sortedByCoord.out.bam' (total=9386614)
[2026-06-08T08:03:19] Marking multi-mapping alignments (marked=6879411)
[2026-06-08T08:03:24] Detecting strandedness (reverse)
[2026-06-08T08:03:24] Assigning strands to alignments 
[2026-06-08T08:03:26] Annotating alignments 
[2026-06-08T08:04:15] Filtering duplicates (remaining=3967024)
[2026-06-08T08:04:24] 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=3580645)
[2026-06-08T08:04:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3580645)
[2026-06-08T08:04:28] Filtering viral contigs with expression lower than the top 5 (remaining=3580645)
[2026-06-08T08:04:33] Filtering viral contigs with less than 5% coverage (remaining=3580645)
[2026-06-08T08:04:36] Estimating fragment length (mate gap mean=-83.1175, mate gap stddev=29.0833, read length mean=118.715)
[2026-06-08T08:04:36] Filtering read-through fragments with a distance <=10000bp (remaining=3451822)
[2026-06-08T08:04:38] Filtering inconsistently clipped mates (remaining=3356311)
[2026-06-08T08:04:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2783268)
[2026-06-08T08:04:45] Filtering fragments with small insert size (remaining=2781873)
[2026-06-08T08:04:47] Filtering alignments with long gaps (remaining=2781873)
[2026-06-08T08:04:50] Filtering fragments with both mates in the same gene (remaining=2780510)
[2026-06-08T08:04:52] Filtering fusions arising from hairpin structures (remaining=2549513)
[2026-06-08T08:04:54] Filtering reads with a mismatch p-value <=0.01 (remaining=757988)
[2026-06-08T08:05:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=487273)
[2026-06-08T08:05:10] Finding fusions and counting supporting reads (total=477256)
[2026-06-08T08:05:29] Merging adjacent fusion breakpoints (remaining=474804)
[2026-06-08T08:05:31] Filtering multi-mapping fusions by alignment score and read support (remaining=199861)
[2026-06-08T08:06:12] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:06:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=198173)
[2026-06-08T08:06:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=153850)
[2026-06-08T08:06:23] Filtering fusions with <2 supporting reads (remaining=7746)
[2026-06-08T08:06:24] Filtering fusions with an e-value >=0.3 (remaining=1734)
[2026-06-08T08:06:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1757)
[2026-06-08T08:06:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1545)
[2026-06-08T08:06:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1545)
[2026-06-08T08:06:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1522)
[2026-06-08T08:06:37] Searching for fusions with spliced split reads (remaining=1613)
[2026-06-08T08:06:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=1241)
[2026-06-08T08:06:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1227)
[2026-06-08T08:06:48] Searching for fusions with >=4 spliced events (remaining=1327)
[2026-06-08T08:06:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=367)
[2026-06-08T08:07:09] Filtering fusions with anchors <=23nt (remaining=320)
[2026-06-08T08:07:10] Filtering end-to-end fusions with low support (remaining=312)
[2026-06-08T08:07:11] Filtering fusions with no coverage around the breakpoints (remaining=307)
[2026-06-08T08:07:11] Indexing gene sequences 
[2026-06-08T08:07:16] Filtering genes with >=30% identity (remaining=100)
[2026-06-08T08:07:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=43)
[2026-06-08T08:07:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=43)
[2026-06-08T08:07:21] Searching for additional isoforms (remaining=46)
[2026-06-08T08:07:22] Assigning confidence scores to events 
[2026-06-08T08:07:27] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:07:27] Writing fusions to file 'tih_rna_sample_00111_23H5VFLT4_s30.arriba.fusions.tsv' 
[2026-06-08T08:07:28] Writing discarded fusions to file 'tih_rna_sample_00111_23H5VFLT4_s30.arriba.fusions.discarded.tsv'
[2026-06-08T08:08:08] Freeing resources
[2026-06-08T08:08:30] Done (elapsed time=00:12:14, CPU time=00:12:12, peak memory=14.5gb)