[2026-06-08T08:32:36] Launching Arriba 2.4.0
[2026-06-08T08:32:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:49] Reading chimeric alignments from 'tih_rna_sample_00755_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11117938)
[2026-06-08T08:39:55] Marking multi-mapping alignments (marked=6875102)
[2026-06-08T08:39:59] Detecting strandedness (reverse)
[2026-06-08T08:39:59] Assigning strands to alignments 
[2026-06-08T08:40:01] Annotating alignments 
[2026-06-08T08:40:36] Filtering duplicates (remaining=7715226)
[2026-06-08T08:40:43] 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=7449523)
[2026-06-08T08:40:46] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7449523)
[2026-06-08T08:40:48] Filtering viral contigs with expression lower than the top 5 (remaining=7449523)
[2026-06-08T08:40:53] Filtering viral contigs with less than 5% coverage (remaining=7449523)
[2026-06-08T08:40:55] Estimating fragment length (mate gap mean=-86.541, mate gap stddev=29.5524, read length mean=136.098)
[2026-06-08T08:40:55] Filtering read-through fragments with a distance <=10000bp (remaining=6981930)
[2026-06-08T08:40:57] Filtering inconsistently clipped mates (remaining=6877539)
[2026-06-08T08:40:59] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6744867)
[2026-06-08T08:41:04] Filtering fragments with small insert size (remaining=6744261)
[2026-06-08T08:41:06] Filtering alignments with long gaps (remaining=6744261)
[2026-06-08T08:41:08] Filtering fragments with both mates in the same gene (remaining=6743209)
[2026-06-08T08:41:10] Filtering fusions arising from hairpin structures (remaining=6384475)
[2026-06-08T08:41:13] Filtering reads with a mismatch p-value <=0.01 (remaining=3256079)
[2026-06-08T08:41:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=1249399)
[2026-06-08T08:41:41] Finding fusions and counting supporting reads (total=884297)
[2026-06-08T08:42:01] Merging adjacent fusion breakpoints (remaining=874744)
[2026-06-08T08:42:03] Filtering multi-mapping fusions by alignment score and read support (remaining=582977)
[2026-06-08T08:42:38] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:42:46] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=581273)
[2026-06-08T08:42:47] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=331600)
[2026-06-08T08:42:48] Filtering fusions with <2 supporting reads (remaining=49268)
[2026-06-08T08:42:49] Filtering fusions with an e-value >=0.3 (remaining=14756)
[2026-06-08T08:42:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14809)
[2026-06-08T08:42:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14746)
[2026-06-08T08:42:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14746)
[2026-06-08T08:42:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8721)
[2026-06-08T08:43:02] Searching for fusions with spliced split reads (remaining=8768)
[2026-06-08T08:43:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=4993)
[2026-06-08T08:43:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4941)
[2026-06-08T08:43:10] Searching for fusions with >=4 spliced events (remaining=6295)
[2026-06-08T08:43:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2742)
[2026-06-08T08:43:27] Filtering fusions with anchors <=23nt (remaining=2249)
[2026-06-08T08:43:28] Filtering end-to-end fusions with low support (remaining=2178)
[2026-06-08T08:43:28] Filtering fusions with no coverage around the breakpoints (remaining=2119)
[2026-06-08T08:43:29] Indexing gene sequences 
[2026-06-08T08:43:37] Filtering genes with >=30% identity (remaining=631)
[2026-06-08T08:43:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=294)
[2026-06-08T08:43:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=241)
[2026-06-08T08:43:51] Searching for additional isoforms (remaining=322)
[2026-06-08T08:43:53] Assigning confidence scores to events 
[2026-06-08T08:43:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:43:57] Writing fusions to file 'tih_rna_sample_00755_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:44:00] Writing discarded fusions to file 'tih_rna_sample_00755_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:44:32] Freeing resources
[2026-06-08T08:44:50] Done (elapsed time=00:12:14, CPU time=00:12:12, peak memory=15.7gb)