[2026-06-08T08:37:35] Launching Arriba 2.4.0
[2026-06-08T08:37:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:37:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:37:50] Reading chimeric alignments from 'tih_rna_sample_00635_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11745889)
[2026-06-08T08:45:26] Marking multi-mapping alignments (marked=7207309)
[2026-06-08T08:45:32] Detecting strandedness (reverse)
[2026-06-08T08:45:32] Assigning strands to alignments 
[2026-06-08T08:45:34] Annotating alignments 
[2026-06-08T08:46:14] Filtering duplicates (remaining=7223093)
[2026-06-08T08:46:22] 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=6928448)
[2026-06-08T08:46:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6928448)
[2026-06-08T08:46:27] Filtering viral contigs with expression lower than the top 5 (remaining=6928448)
[2026-06-08T08:46:32] Filtering viral contigs with less than 5% coverage (remaining=6928448)
[2026-06-08T08:46:35] Estimating fragment length (mate gap mean=-86.1714, mate gap stddev=30.7388, read length mean=134.794)
[2026-06-08T08:46:35] Filtering read-through fragments with a distance <=10000bp (remaining=6563849)
[2026-06-08T08:46:38] Filtering inconsistently clipped mates (remaining=6460379)
[2026-06-08T08:46:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6315820)
[2026-06-08T08:46:45] Filtering fragments with small insert size (remaining=6314953)
[2026-06-08T08:46:47] Filtering alignments with long gaps (remaining=6314953)
[2026-06-08T08:46:50] Filtering fragments with both mates in the same gene (remaining=6313925)
[2026-06-08T08:46:53] Filtering fusions arising from hairpin structures (remaining=5950392)
[2026-06-08T08:46:56] Filtering reads with a mismatch p-value <=0.01 (remaining=2984589)
[2026-06-08T08:47:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=997718)
[2026-06-08T08:47:25] Finding fusions and counting supporting reads (total=708865)
[2026-06-08T08:47:43] Merging adjacent fusion breakpoints (remaining=700247)
[2026-06-08T08:47:45] Filtering multi-mapping fusions by alignment score and read support (remaining=460227)
[2026-06-08T08:48:22] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:48:29] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=457827)
[2026-06-08T08:48:30] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=247644)
[2026-06-08T08:48:31] Filtering fusions with <2 supporting reads (remaining=40134)
[2026-06-08T08:48:32] Filtering fusions with an e-value >=0.3 (remaining=13411)
[2026-06-08T08:48:33] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13476)
[2026-06-08T08:48:37] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13328)
[2026-06-08T08:48:37] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13329)
[2026-06-08T08:48:39] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9002)
[2026-06-08T08:48:45] Searching for fusions with spliced split reads (remaining=9023)
[2026-06-08T08:48:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=5514)
[2026-06-08T08:48:54] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5417)
[2026-06-08T08:48:55] Searching for fusions with >=4 spliced events (remaining=6401)
[2026-06-08T08:48:56] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2341)
[2026-06-08T08:49:28] Filtering fusions with anchors <=23nt (remaining=1598)
[2026-06-08T08:49:28] Filtering end-to-end fusions with low support (remaining=1535)
[2026-06-08T08:49:29] Filtering fusions with no coverage around the breakpoints (remaining=1473)
[2026-06-08T08:49:30] Indexing gene sequences 
[2026-06-08T08:49:37] Filtering genes with >=30% identity (remaining=409)
[2026-06-08T08:49:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=169)
[2026-06-08T08:49:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=145)
[2026-06-08T08:49:46] Searching for additional isoforms (remaining=198)
[2026-06-08T08:49:47] Assigning confidence scores to events 
[2026-06-08T08:49:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:49:51] Writing fusions to file 'tih_rna_sample_00635_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:49:53] Writing discarded fusions to file 'tih_rna_sample_00635_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:33] Freeing resources
[2026-06-08T08:50:56] Done (elapsed time=00:13:21, CPU time=00:13:20, peak memory=16.3gb)