[2026-06-08T08:38:28] Launching Arriba 2.4.0
[2026-06-08T08:38:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:38:37] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:38:40] Reading chimeric alignments from 'tih_rna_sample_00664_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10454390)
[2026-06-08T08:44:47] Marking multi-mapping alignments (marked=6513424)
[2026-06-08T08:44:51] Detecting strandedness (reverse)
[2026-06-08T08:44:51] Assigning strands to alignments 
[2026-06-08T08:44:53] Annotating alignments 
[2026-06-08T08:45:26] Filtering duplicates (remaining=7158784)
[2026-06-08T08:45:34] 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=6804135)
[2026-06-08T08:45:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6804135)
[2026-06-08T08:45:38] Filtering viral contigs with expression lower than the top 5 (remaining=6804135)
[2026-06-08T08:45:43] Filtering viral contigs with less than 5% coverage (remaining=6804135)
[2026-06-08T08:45:45] Estimating fragment length (mate gap mean=-87.2332, mate gap stddev=28.9321, read length mean=133.567)
[2026-06-08T08:45:45] Filtering read-through fragments with a distance <=10000bp (remaining=6359532)
[2026-06-08T08:45:47] Filtering inconsistently clipped mates (remaining=6269831)
[2026-06-08T08:45:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6150426)
[2026-06-08T08:45:54] Filtering fragments with small insert size (remaining=6149793)
[2026-06-08T08:45:56] Filtering alignments with long gaps (remaining=6149793)
[2026-06-08T08:45:58] Filtering fragments with both mates in the same gene (remaining=6148821)
[2026-06-08T08:46:00] Filtering fusions arising from hairpin structures (remaining=5834707)
[2026-06-08T08:46:03] Filtering reads with a mismatch p-value <=0.01 (remaining=2917581)
[2026-06-08T08:46:18] Filtering reads with low entropy (k-mer content >=60%) (remaining=1175293)
[2026-06-08T08:46:29] Finding fusions and counting supporting reads (total=820460)
[2026-06-08T08:46:47] Merging adjacent fusion breakpoints (remaining=812805)
[2026-06-08T08:46:49] Filtering multi-mapping fusions by alignment score and read support (remaining=531736)
[2026-06-08T08:47:24] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:47:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=530019)
[2026-06-08T08:47:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=292645)
[2026-06-08T08:47:34] Filtering fusions with <2 supporting reads (remaining=40333)
[2026-06-08T08:47:35] Filtering fusions with an e-value >=0.3 (remaining=10363)
[2026-06-08T08:47:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10413)
[2026-06-08T08:47:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10337)
[2026-06-08T08:47:41] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10337)
[2026-06-08T08:47:42] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8959)
[2026-06-08T08:47:47] Searching for fusions with spliced split reads (remaining=9100)
[2026-06-08T08:47:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=5343)
[2026-06-08T08:47:54] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5282)
[2026-06-08T08:47:55] Searching for fusions with >=4 spliced events (remaining=6494)
[2026-06-08T08:47:57] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2664)
[2026-06-08T08:48:11] Filtering fusions with anchors <=23nt (remaining=2158)
[2026-06-08T08:48:12] Filtering end-to-end fusions with low support (remaining=2082)
[2026-06-08T08:48:13] Filtering fusions with no coverage around the breakpoints (remaining=2025)
[2026-06-08T08:48:13] Indexing gene sequences 
[2026-06-08T08:48:20] Filtering genes with >=30% identity (remaining=622)
[2026-06-08T08:48:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=260)
[2026-06-08T08:48:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=240)
[2026-06-08T08:48:28] Searching for additional isoforms (remaining=313)
[2026-06-08T08:48:30] Assigning confidence scores to events 
[2026-06-08T08:48:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:48:34] Writing fusions to file 'tih_rna_sample_00664_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:48:36] Writing discarded fusions to file 'tih_rna_sample_00664_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:49:09] Freeing resources
[2026-06-08T08:49:26] Done (elapsed time=00:10:58, CPU time=00:10:56, peak memory=15.1gb)