[2026-06-08T07:32:59] Launching Arriba 2.4.0
[2026-06-08T07:32:59] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:33:16] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:33:22] Reading chimeric alignments from 'tih_rna_sample_00677_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=1751072)
[2026-06-08T07:34:14] Marking multi-mapping alignments (marked=1368784)
[2026-06-08T07:34:15] Detecting strandedness (reverse)
[2026-06-08T07:34:15] Assigning strands to alignments 
[2026-06-08T07:34:15] Annotating alignments 
[2026-06-08T07:34:20] Filtering duplicates (remaining=534542)
[2026-06-08T07:34:21] 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=435303)
[2026-06-08T07:34:21] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=435303)
[2026-06-08T07:34:22] Filtering viral contigs with expression lower than the top 5 (remaining=435303)
[2026-06-08T07:34:22] Filtering viral contigs with less than 5% coverage (remaining=435303)
[2026-06-08T07:34:23] Estimating fragment length (mate gap mean=-74.8198, mate gap stddev=28.8702, read length mean=107.187)
[2026-06-08T07:34:23] Filtering read-through fragments with a distance <=10000bp (remaining=413106)
[2026-06-08T07:34:23] Filtering inconsistently clipped mates (remaining=394656)
[2026-06-08T07:34:24] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=383389)
[2026-06-08T07:34:24] Filtering fragments with small insert size (remaining=383133)
[2026-06-08T07:34:24] Filtering alignments with long gaps (remaining=383133)
[2026-06-08T07:34:25] Filtering fragments with both mates in the same gene (remaining=383022)
[2026-06-08T07:34:25] Filtering fusions arising from hairpin structures (remaining=347117)
[2026-06-08T07:34:25] Filtering reads with a mismatch p-value <=0.01 (remaining=108063)
[2026-06-08T07:34:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=32605)
[2026-06-08T07:34:27] Finding fusions and counting supporting reads (total=28737)
[2026-06-08T07:34:30] Merging adjacent fusion breakpoints (remaining=28235)
[2026-06-08T07:34:30] Filtering multi-mapping fusions by alignment score and read support (remaining=14970)
[2026-06-08T07:34:35] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:34:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=14820)
[2026-06-08T07:34:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=7612)
[2026-06-08T07:34:36] Filtering fusions with <2 supporting reads (remaining=497)
[2026-06-08T07:34:36] Filtering fusions with an e-value >=0.3 (remaining=236)
[2026-06-08T07:34:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=248)
[2026-06-08T07:34:37] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=228)
[2026-06-08T07:34:37] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=228)
[2026-06-08T07:34:37] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=194)
[2026-06-08T07:34:37] Searching for fusions with spliced split reads (remaining=205)
[2026-06-08T07:34:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=173)
[2026-06-08T07:34:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=171)
[2026-06-08T07:34:38] Searching for fusions with >=4 spliced events (remaining=174)
[2026-06-08T07:34:38] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=41)
[2026-06-08T07:34:58] Filtering fusions with anchors <=23nt (remaining=24)
[2026-06-08T07:34:58] Filtering end-to-end fusions with low support (remaining=22)
[2026-06-08T07:34:58] Filtering fusions with no coverage around the breakpoints (remaining=19)
[2026-06-08T07:34:58] Indexing gene sequences 
[2026-06-08T07:34:59] Filtering genes with >=30% identity (remaining=14)
[2026-06-08T07:34:59] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=6)
[2026-06-08T07:34:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=6)
[2026-06-08T07:34:59] Searching for additional isoforms (remaining=6)
[2026-06-08T07:34:59] Assigning confidence scores to events 
[2026-06-08T07:35:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:35:00] Writing fusions to file 'tih_rna_sample_00677_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T07:35:00] Writing discarded fusions to file 'tih_rna_sample_00677_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:35:03] Freeing resources
[2026-06-08T07:35:07] Done (elapsed time=00:02:08, CPU time=00:02:08, peak memory=5.87gb)