[2026-06-08T08:52:36] Launching Arriba 2.4.0
[2026-06-08T08:52:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:49] Reading chimeric alignments from 'tih_rna_sample_00739_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=12278160)
[2026-06-08T09:00:13] Marking multi-mapping alignments (marked=7904593)
[2026-06-08T09:00:18] Detecting strandedness (reverse)
[2026-06-08T09:00:18] Assigning strands to alignments 
[2026-06-08T09:00:21] Annotating alignments 
[2026-06-08T09:01:00] Filtering duplicates (remaining=8270904)
[2026-06-08T09:01:09] 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=7812411)
[2026-06-08T09:01:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7812411)
[2026-06-08T09:01:14] Filtering viral contigs with expression lower than the top 5 (remaining=7812411)
[2026-06-08T09:01:20] Filtering viral contigs with less than 5% coverage (remaining=7812411)
[2026-06-08T09:01:23] Estimating fragment length (mate gap mean=-84.7546, mate gap stddev=30.9416, read length mean=135.422)
[2026-06-08T09:01:23] Filtering read-through fragments with a distance <=10000bp (remaining=7353913)
[2026-06-08T09:01:25] Filtering inconsistently clipped mates (remaining=7243555)
[2026-06-08T09:01:28] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7083886)
[2026-06-08T09:01:34] Filtering fragments with small insert size (remaining=7082940)
[2026-06-08T09:01:36] Filtering alignments with long gaps (remaining=7082940)
[2026-06-08T09:01:39] Filtering fragments with both mates in the same gene (remaining=7081852)
[2026-06-08T09:01:42] Filtering fusions arising from hairpin structures (remaining=6665223)
[2026-06-08T09:01:45] Filtering reads with a mismatch p-value <=0.01 (remaining=3315912)
[2026-06-08T09:02:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=1169832)
[2026-06-08T09:02:16] Finding fusions and counting supporting reads (total=855053)
[2026-06-08T09:02:37] Merging adjacent fusion breakpoints (remaining=847008)
[2026-06-08T09:02:40] Filtering multi-mapping fusions by alignment score and read support (remaining=543786)
[2026-06-08T09:03:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:03:29] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=541273)
[2026-06-08T09:03:30] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=305477)
[2026-06-08T09:03:32] Filtering fusions with <2 supporting reads (remaining=44434)
[2026-06-08T09:03:33] Filtering fusions with an e-value >=0.3 (remaining=15698)
[2026-06-08T09:03:34] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=15758)
[2026-06-08T09:03:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=15675)
[2026-06-08T09:03:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=15675)
[2026-06-08T09:03:42] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10084)
[2026-06-08T09:03:48] Searching for fusions with spliced split reads (remaining=10101)
[2026-06-08T09:03:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=5031)
[2026-06-08T09:03:56] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4987)
[2026-06-08T09:03:57] Searching for fusions with >=4 spliced events (remaining=6006)
[2026-06-08T09:03:59] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2153)
[2026-06-08T09:04:14] Filtering fusions with anchors <=23nt (remaining=1677)
[2026-06-08T09:04:15] Filtering end-to-end fusions with low support (remaining=1629)
[2026-06-08T09:04:16] Filtering fusions with no coverage around the breakpoints (remaining=1600)
[2026-06-08T09:04:17] Indexing gene sequences 
[2026-06-08T09:04:23] Filtering genes with >=30% identity (remaining=515)
[2026-06-08T09:04:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=250)
[2026-06-08T09:04:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=214)
[2026-06-08T09:04:32] Searching for additional isoforms (remaining=292)
[2026-06-08T09:04:33] Assigning confidence scores to events 
[2026-06-08T09:04:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:04:38] Writing fusions to file 'tih_rna_sample_00739_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:04:40] Writing discarded fusions to file 'tih_rna_sample_00739_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:05:17] Freeing resources
[2026-06-08T09:05:36] Done (elapsed time=00:13:00, CPU time=00:12:59, peak memory=17gb)