[2026-06-08T08:49:36] Launching Arriba 2.4.0
[2026-06-08T08:49:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:52] Reading chimeric alignments from 'tih_rna_sample_00574_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11305547)
[2026-06-08T08:59:45] Marking multi-mapping alignments (marked=6814705)
[2026-06-08T08:59:53] Detecting strandedness (reverse)
[2026-06-08T08:59:53] Assigning strands to alignments 
[2026-06-08T08:59:56] Annotating alignments 
[2026-06-08T09:01:09] Filtering duplicates (remaining=7674910)
[2026-06-08T09:01:21] 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=7366535)
[2026-06-08T09:01:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7366535)
[2026-06-08T09:01:28] Filtering viral contigs with expression lower than the top 5 (remaining=7366535)
[2026-06-08T09:01:37] Filtering viral contigs with less than 5% coverage (remaining=7366535)
[2026-06-08T09:01:41] Estimating fragment length (mate gap mean=-87.523, mate gap stddev=28.9849, read length mean=134.751)
[2026-06-08T09:01:42] Filtering read-through fragments with a distance <=10000bp (remaining=6828555)
[2026-06-08T09:01:46] Filtering inconsistently clipped mates (remaining=6715483)
[2026-06-08T09:01:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6574269)
[2026-06-08T09:01:58] Filtering fragments with small insert size (remaining=6573299)
[2026-06-08T09:02:02] Filtering alignments with long gaps (remaining=6573299)
[2026-06-08T09:02:07] Filtering fragments with both mates in the same gene (remaining=6572228)
[2026-06-08T09:02:12] Filtering fusions arising from hairpin structures (remaining=6215903)
[2026-06-08T09:02:17] Filtering reads with a mismatch p-value <=0.01 (remaining=3247122)
[2026-06-08T09:02:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=1199488)
[2026-06-08T09:03:02] Finding fusions and counting supporting reads (total=888198)
[2026-06-08T09:03:35] Merging adjacent fusion breakpoints (remaining=876629)
[2026-06-08T09:03:39] Filtering multi-mapping fusions by alignment score and read support (remaining=570550)
[2026-06-08T09:04:32] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:04:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=567806)
[2026-06-08T09:04:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=298608)
[2026-06-08T09:04:52] Filtering fusions with <2 supporting reads (remaining=41156)
[2026-06-08T09:04:53] Filtering fusions with an e-value >=0.3 (remaining=11591)
[2026-06-08T09:04:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11648)
[2026-06-08T09:05:01] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11567)
[2026-06-08T09:05:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11567)
[2026-06-08T09:05:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8930)
[2026-06-08T09:05:15] Searching for fusions with spliced split reads (remaining=8943)
[2026-06-08T09:05:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=5270)
[2026-06-08T09:05:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5207)
[2026-06-08T09:05:29] Searching for fusions with >=4 spliced events (remaining=6449)
[2026-06-08T09:05:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2703)
[2026-06-08T09:05:55] Filtering fusions with anchors <=23nt (remaining=2243)
[2026-06-08T09:05:56] Filtering end-to-end fusions with low support (remaining=2189)
[2026-06-08T09:05:58] Filtering fusions with no coverage around the breakpoints (remaining=2140)
[2026-06-08T09:05:59] Indexing gene sequences 
[2026-06-08T09:06:12] Filtering genes with >=30% identity (remaining=638)
[2026-06-08T09:06:19] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=311)
[2026-06-08T09:06:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=261)
[2026-06-08T09:06:35] Searching for additional isoforms (remaining=358)
[2026-06-08T09:06:38] Assigning confidence scores to events 
[2026-06-08T09:06:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:06:44] Writing fusions to file 'tih_rna_sample_00574_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:06:49] Writing discarded fusions to file 'tih_rna_sample_00574_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:07:49] Freeing resources
[2026-06-08T09:08:19] Done (elapsed time=00:18:43, CPU time=00:18:42, peak memory=15.9gb)