[2026-06-08T08:55:34] Launching Arriba 2.4.0
[2026-06-08T08:55:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:55:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:55:52] Reading chimeric alignments from 'tih_rna_sample_00650_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11226205)
[2026-06-08T09:03:01] Marking multi-mapping alignments (marked=6923165)
[2026-06-08T09:03:05] Detecting strandedness (reverse)
[2026-06-08T09:03:05] Assigning strands to alignments 
[2026-06-08T09:03:07] Annotating alignments 
[2026-06-08T09:03:41] Filtering duplicates (remaining=7603712)
[2026-06-08T09:03:49] 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=7298400)
[2026-06-08T09:03:52] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7298400)
[2026-06-08T09:03:53] Filtering viral contigs with expression lower than the top 5 (remaining=7298400)
[2026-06-08T09:03:58] Filtering viral contigs with less than 5% coverage (remaining=7298400)
[2026-06-08T09:04:00] Estimating fragment length (mate gap mean=-86.2686, mate gap stddev=31.5625, read length mean=138.083)
[2026-06-08T09:04:00] Filtering read-through fragments with a distance <=10000bp (remaining=6876828)
[2026-06-08T09:04:02] Filtering inconsistently clipped mates (remaining=6779594)
[2026-06-08T09:04:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6605708)
[2026-06-08T09:04:09] Filtering fragments with small insert size (remaining=6605180)
[2026-06-08T09:04:11] Filtering alignments with long gaps (remaining=6605180)
[2026-06-08T09:04:13] Filtering fragments with both mates in the same gene (remaining=6603814)
[2026-06-08T09:04:15] Filtering fusions arising from hairpin structures (remaining=6223962)
[2026-06-08T09:04:18] Filtering reads with a mismatch p-value <=0.01 (remaining=3246662)
[2026-06-08T09:04:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=1117339)
[2026-06-08T09:04:46] Finding fusions and counting supporting reads (total=829158)
[2026-06-08T09:05:04] Merging adjacent fusion breakpoints (remaining=822984)
[2026-06-08T09:05:06] Filtering multi-mapping fusions by alignment score and read support (remaining=521152)
[2026-06-08T09:05:38] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:05:45] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=516126)
[2026-06-08T09:05:46] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=305447)
[2026-06-08T09:05:47] Filtering fusions with <2 supporting reads (remaining=47483)
[2026-06-08T09:05:47] Filtering fusions with an e-value >=0.3 (remaining=22765)
[2026-06-08T09:05:48] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=22834)
[2026-06-08T09:05:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=22730)
[2026-06-08T09:05:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=22732)
[2026-06-08T09:05:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8971)
[2026-06-08T09:06:01] Searching for fusions with spliced split reads (remaining=9033)
[2026-06-08T09:06:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=4670)
[2026-06-08T09:06:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4600)
[2026-06-08T09:06:09] Searching for fusions with >=4 spliced events (remaining=5509)
[2026-06-08T09:06:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2232)
[2026-06-08T09:06:27] Filtering fusions with anchors <=23nt (remaining=1754)
[2026-06-08T09:06:28] Filtering end-to-end fusions with low support (remaining=1692)
[2026-06-08T09:06:29] Filtering fusions with no coverage around the breakpoints (remaining=1632)
[2026-06-08T09:06:30] Indexing gene sequences 
[2026-06-08T09:06:37] Filtering genes with >=30% identity (remaining=462)
[2026-06-08T09:06:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=221)
[2026-06-08T09:06:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=187)
[2026-06-08T09:06:53] Searching for additional isoforms (remaining=253)
[2026-06-08T09:06:54] Assigning confidence scores to events 
[2026-06-08T09:06:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:06:58] Writing fusions to file 'tih_rna_sample_00650_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:06:59] Writing discarded fusions to file 'tih_rna_sample_00650_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:07:32] Freeing resources
[2026-06-08T09:07:50] Done (elapsed time=00:12:16, CPU time=00:12:15, peak memory=15.9gb)