[2026-06-08T08:13:14] Launching Arriba 2.4.0
[2026-06-08T08:13:14] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:13:23] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:13:27] Reading chimeric alignments from 'tih_rna_sample_00598_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=9608885)
[2026-06-08T08:17:26] Marking multi-mapping alignments (marked=6858829)
[2026-06-08T08:17:30] Detecting strandedness (no)
[2026-06-08T08:17:30] Annotating alignments 
[2026-06-08T08:18:03] Filtering duplicates (remaining=3184433)
[2026-06-08T08:18:08] 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=2834575)
[2026-06-08T08:18:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2834575)
[2026-06-08T08:18:11] Filtering viral contigs with expression lower than the top 5 (remaining=2834575)
[2026-06-08T08:18:15] Filtering viral contigs with less than 5% coverage (remaining=2834575)
[2026-06-08T08:18:17] Estimating fragment length (mate gap mean=-84.5628, mate gap stddev=28.2214, read length mean=120.876)
[2026-06-08T08:18:17] Filtering read-through fragments with a distance <=10000bp (remaining=2740247)
[2026-06-08T08:18:19] Filtering inconsistently clipped mates (remaining=2678791)
[2026-06-08T08:18:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2585962)
[2026-06-08T08:18:23] Filtering fragments with small insert size (remaining=2585050)
[2026-06-08T08:18:25] Filtering alignments with long gaps (remaining=2585050)
[2026-06-08T08:18:26] Filtering fragments with both mates in the same gene (remaining=2584396)
[2026-06-08T08:18:28] Filtering fusions arising from hairpin structures (remaining=2428895)
[2026-06-08T08:18:30] Filtering reads with a mismatch p-value <=0.01 (remaining=960372)
[2026-06-08T08:18:37] Filtering reads with low entropy (k-mer content >=60%) (remaining=284579)
[2026-06-08T08:18:43] Finding fusions and counting supporting reads (total=242962)
[2026-06-08T08:18:53] Merging adjacent fusion breakpoints (remaining=240511)
[2026-06-08T08:18:54] Filtering multi-mapping fusions by alignment score and read support (remaining=127180)
[2026-06-08T08:19:23] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:19:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=126293)
[2026-06-08T08:19:26] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=77885)
[2026-06-08T08:19:27] Filtering fusions with <2 supporting reads (remaining=7407)
[2026-06-08T08:19:27] Filtering fusions with an e-value >=0.3 (remaining=1905)
[2026-06-08T08:19:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1938)
[2026-06-08T08:19:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1879)
[2026-06-08T08:19:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1879)
[2026-06-08T08:19:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1860)
[2026-06-08T08:19:35] Searching for fusions with spliced split reads (remaining=1902)
[2026-06-08T08:19:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=1437)
[2026-06-08T08:19:39] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1419)
[2026-06-08T08:19:39] Searching for fusions with >=4 spliced events (remaining=1533)
[2026-06-08T08:19:40] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=489)
[2026-06-08T08:19:51] Filtering fusions with anchors <=23nt (remaining=394)
[2026-06-08T08:19:52] Filtering end-to-end fusions with low support (remaining=380)
[2026-06-08T08:19:52] Filtering fusions with no coverage around the breakpoints (remaining=365)
[2026-06-08T08:19:52] Indexing gene sequences 
[2026-06-08T08:19:55] Filtering genes with >=30% identity (remaining=113)
[2026-06-08T08:19:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=64)
[2026-06-08T08:19:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=61)
[2026-06-08T08:19:57] Searching for additional isoforms (remaining=75)
[2026-06-08T08:19:58] Assigning confidence scores to events 
[2026-06-08T08:20:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:20:00] Writing fusions to file 'tih_rna_sample_00598_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:20:00] Writing discarded fusions to file 'tih_rna_sample_00598_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:20:15] Freeing resources
[2026-06-08T08:20:28] Done (elapsed time=00:07:14, CPU time=00:07:13, peak memory=13.9gb)