[2026-06-08T08:39:28] Launching Arriba 2.4.0
[2026-06-08T08:39:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:43] Reading chimeric alignments from 'tih_rna_sample_00694_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10867490)
[2026-06-08T08:45:27] Marking multi-mapping alignments (marked=7273264)
[2026-06-08T08:45:31] Detecting strandedness (reverse)
[2026-06-08T08:45:31] Assigning strands to alignments 
[2026-06-08T08:45:33] Annotating alignments 
[2026-06-08T08:46:04] Filtering duplicates (remaining=5923543)
[2026-06-08T08:46:10] 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=5563885)
[2026-06-08T08:46:12] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5563885)
[2026-06-08T08:46:14] Filtering viral contigs with expression lower than the top 5 (remaining=5563885)
[2026-06-08T08:46:18] Filtering viral contigs with less than 5% coverage (remaining=5563885)
[2026-06-08T08:46:20] Estimating fragment length (mate gap mean=-85.9002, mate gap stddev=29.5121, read length mean=130.518)
[2026-06-08T08:46:21] Filtering read-through fragments with a distance <=10000bp (remaining=5305277)
[2026-06-08T08:46:22] Filtering inconsistently clipped mates (remaining=5211067)
[2026-06-08T08:46:24] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5092384)
[2026-06-08T08:46:27] Filtering fragments with small insert size (remaining=5091494)
[2026-06-08T08:46:29] Filtering alignments with long gaps (remaining=5091494)
[2026-06-08T08:46:31] Filtering fragments with both mates in the same gene (remaining=5090654)
[2026-06-08T08:46:33] Filtering fusions arising from hairpin structures (remaining=4777602)
[2026-06-08T08:46:35] Filtering reads with a mismatch p-value <=0.01 (remaining=2205940)
[2026-06-08T08:46:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=654447)
[2026-06-08T08:46:55] Finding fusions and counting supporting reads (total=522958)
[2026-06-08T08:47:09] Merging adjacent fusion breakpoints (remaining=517503)
[2026-06-08T08:47:10] Filtering multi-mapping fusions by alignment score and read support (remaining=315302)
[2026-06-08T08:47:38] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:47:44] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=313712)
[2026-06-08T08:47:44] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=174589)
[2026-06-08T08:47:45] Filtering fusions with <2 supporting reads (remaining=21299)
[2026-06-08T08:47:45] Filtering fusions with an e-value >=0.3 (remaining=7694)
[2026-06-08T08:47:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7757)
[2026-06-08T08:47:49] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7709)
[2026-06-08T08:47:50] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7709)
[2026-06-08T08:47:51] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4284)
[2026-06-08T08:47:56] Searching for fusions with spliced split reads (remaining=4376)
[2026-06-08T08:48:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=2969)
[2026-06-08T08:48:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2944)
[2026-06-08T08:48:02] Searching for fusions with >=4 spliced events (remaining=3316)
[2026-06-08T08:48:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1193)
[2026-06-08T08:48:16] Filtering fusions with anchors <=23nt (remaining=951)
[2026-06-08T08:48:17] Filtering end-to-end fusions with low support (remaining=919)
[2026-06-08T08:48:17] Filtering fusions with no coverage around the breakpoints (remaining=891)
[2026-06-08T08:48:18] Indexing gene sequences 
[2026-06-08T08:48:22] Filtering genes with >=30% identity (remaining=323)
[2026-06-08T08:48:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=159)
[2026-06-08T08:48:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=151)
[2026-06-08T08:48:26] Searching for additional isoforms (remaining=186)
[2026-06-08T08:48:27] Assigning confidence scores to events 
[2026-06-08T08:48:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:48:30] Writing fusions to file 'tih_rna_sample_00694_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:48:31] Writing discarded fusions to file 'tih_rna_sample_00694_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:48:54] Freeing resources
[2026-06-08T08:49:10] Done (elapsed time=00:09:42, CPU time=00:09:42, peak memory=15.3gb)