[2026-06-08T08:42:16] Launching Arriba 2.4.0
[2026-06-08T08:42:16] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:42:25] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:42:28] Reading chimeric alignments from 'tih_rna_sample_00742_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=6794068)
[2026-06-08T08:46:28] Marking multi-mapping alignments (marked=4158290)
[2026-06-08T08:46:30] Detecting strandedness (reverse)
[2026-06-08T08:46:30] Assigning strands to alignments 
[2026-06-08T08:46:32] Annotating alignments 
[2026-06-08T08:46:58] Filtering duplicates (remaining=4681314)
[2026-06-08T08:47:04] 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=4482143)
[2026-06-08T08:47:07] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4482143)
[2026-06-08T08:47:08] Filtering viral contigs with expression lower than the top 5 (remaining=4482143)
[2026-06-08T08:47:13] Filtering viral contigs with less than 5% coverage (remaining=4482143)
[2026-06-08T08:47:17] Estimating fragment length (mate gap mean=-86.4456, mate gap stddev=29.9771, read length mean=134.875)
[2026-06-08T08:47:17] Filtering read-through fragments with a distance <=10000bp (remaining=4204833)
[2026-06-08T08:47:19] Filtering inconsistently clipped mates (remaining=4148423)
[2026-06-08T08:47:22] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4061333)
[2026-06-08T08:47:25] Filtering fragments with small insert size (remaining=4060887)
[2026-06-08T08:47:26] Filtering alignments with long gaps (remaining=4060887)
[2026-06-08T08:47:28] Filtering fragments with both mates in the same gene (remaining=4060144)
[2026-06-08T08:47:30] Filtering fusions arising from hairpin structures (remaining=3856915)
[2026-06-08T08:47:32] Filtering reads with a mismatch p-value <=0.01 (remaining=1967749)
[2026-06-08T08:47:45] Filtering reads with low entropy (k-mer content >=60%) (remaining=745973)
[2026-06-08T08:47:55] Finding fusions and counting supporting reads (total=557048)
[2026-06-08T08:48:15] Merging adjacent fusion breakpoints (remaining=553240)
[2026-06-08T08:48:16] Filtering multi-mapping fusions by alignment score and read support (remaining=370292)
[2026-06-08T08:48:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:48:52] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=368320)
[2026-06-08T08:48:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=199941)
[2026-06-08T08:48:54] Filtering fusions with <2 supporting reads (remaining=33968)
[2026-06-08T08:48:54] Filtering fusions with an e-value >=0.3 (remaining=13526)
[2026-06-08T08:48:55] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13565)
[2026-06-08T08:48:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13531)
[2026-06-08T08:48:58] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13531)
[2026-06-08T08:49:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6793)
[2026-06-08T08:49:04] Searching for fusions with spliced split reads (remaining=6921)
[2026-06-08T08:49:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=4193)
[2026-06-08T08:49:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4145)
[2026-06-08T08:49:09] Searching for fusions with >=4 spliced events (remaining=4842)
[2026-06-08T08:49:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1387)
[2026-06-08T08:49:23] Filtering fusions with anchors <=23nt (remaining=1112)
[2026-06-08T08:49:24] Filtering end-to-end fusions with low support (remaining=1081)
[2026-06-08T08:49:25] Filtering fusions with no coverage around the breakpoints (remaining=1046)
[2026-06-08T08:49:25] Indexing gene sequences 
[2026-06-08T08:49:30] Filtering genes with >=30% identity (remaining=331)
[2026-06-08T08:49:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=183)
[2026-06-08T08:49:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=180)
[2026-06-08T08:49:40] Searching for additional isoforms (remaining=209)
[2026-06-08T08:49:41] Assigning confidence scores to events 
[2026-06-08T08:49:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:49:44] Writing fusions to file 'tih_rna_sample_00742_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:49:46] Writing discarded fusions to file 'tih_rna_sample_00742_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:11] Freeing resources
[2026-06-08T08:50:25] Done (elapsed time=00:08:09, CPU time=00:08:07, peak memory=11.2gb)