[2026-06-08T08:16:41] Launching Arriba 2.4.0
[2026-06-08T08:16:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:16:56] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:17:01] Reading chimeric alignments from 'tih_rna_sample_00251_23H5VFLT4_s03.Aligned.sortedByCoord.out.bam' (total=11660419)
[2026-06-08T08:25:55] Marking multi-mapping alignments (marked=8134218)
[2026-06-08T08:26:01] Detecting strandedness (no)
[2026-06-08T08:26:01] Annotating alignments 
[2026-06-08T08:26:54] Filtering duplicates (remaining=6672163)
[2026-06-08T08:27:03] 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=6029103)
[2026-06-08T08:27:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6029103)
[2026-06-08T08:27:08] Filtering viral contigs with expression lower than the top 5 (remaining=6029103)
[2026-06-08T08:27:14] Filtering viral contigs with less than 5% coverage (remaining=6029103)
[2026-06-08T08:27:17] Estimating fragment length (mate gap mean=-85.5081, mate gap stddev=29.55, read length mean=126.528)
[2026-06-08T08:27:17] Filtering read-through fragments with a distance <=10000bp (remaining=5704475)
[2026-06-08T08:27:19] Filtering inconsistently clipped mates (remaining=5564333)
[2026-06-08T08:27:22] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5044265)
[2026-06-08T08:27:28] Filtering fragments with small insert size (remaining=5042739)
[2026-06-08T08:27:30] Filtering alignments with long gaps (remaining=5042739)
[2026-06-08T08:27:33] Filtering fragments with both mates in the same gene (remaining=5041107)
[2026-06-08T08:27:36] Filtering fusions arising from hairpin structures (remaining=4541329)
[2026-06-08T08:27:39] Filtering reads with a mismatch p-value <=0.01 (remaining=1851955)
[2026-06-08T08:27:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=1131935)
[2026-06-08T08:28:04] Finding fusions and counting supporting reads (total=957042)
[2026-06-08T08:28:23] Merging adjacent fusion breakpoints (remaining=950841)
[2026-06-08T08:28:25] Filtering multi-mapping fusions by alignment score and read support (remaining=503900)
[2026-06-08T08:29:05] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:29:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=500507)
[2026-06-08T08:29:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=324276)
[2026-06-08T08:29:16] Filtering fusions with <2 supporting reads (remaining=26674)
[2026-06-08T08:29:17] Filtering fusions with an e-value >=0.3 (remaining=6196)
[2026-06-08T08:29:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6249)
[2026-06-08T08:29:23] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5916)
[2026-06-08T08:29:24] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5916)
[2026-06-08T08:29:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5288)
[2026-06-08T08:29:32] Searching for fusions with spliced split reads (remaining=5306)
[2026-06-08T08:29:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=3743)
[2026-06-08T08:29:41] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3695)
[2026-06-08T08:29:42] Searching for fusions with >=4 spliced events (remaining=4575)
[2026-06-08T08:29:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1911)
[2026-06-08T08:30:02] Filtering fusions with anchors <=23nt (remaining=1587)
[2026-06-08T08:30:02] Filtering end-to-end fusions with low support (remaining=1518)
[2026-06-08T08:30:03] Filtering fusions with no coverage around the breakpoints (remaining=1498)
[2026-06-08T08:30:04] Indexing gene sequences 
[2026-06-08T08:30:13] Filtering genes with >=30% identity (remaining=562)
[2026-06-08T08:30:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=337)
[2026-06-08T08:30:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=247)
[2026-06-08T08:30:27] Searching for additional isoforms (remaining=339)
[2026-06-08T08:30:28] Assigning confidence scores to events 
[2026-06-08T08:30:34] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:30:34] Writing fusions to file 'tih_rna_sample_00251_23H5VFLT4_s03.arriba.fusions.tsv' 
[2026-06-08T08:30:38] Writing discarded fusions to file 'tih_rna_sample_00251_23H5VFLT4_s03.arriba.fusions.discarded.tsv'
[2026-06-08T08:31:20] Freeing resources
[2026-06-08T08:31:44] Done (elapsed time=00:15:03, CPU time=00:15:02, peak memory=17gb)