[2026-06-08T08:49:34] Launching Arriba 2.4.0
[2026-06-08T08:49:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:43] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:47] Reading chimeric alignments from 'tih_rna_sample_00649_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11605399)
[2026-06-08T08:56:50] Marking multi-mapping alignments (marked=7303890)
[2026-06-08T08:56:55] Detecting strandedness (reverse)
[2026-06-08T08:56:55] Assigning strands to alignments 
[2026-06-08T08:56:58] Annotating alignments 
[2026-06-08T08:57:36] Filtering duplicates (remaining=7798358)
[2026-06-08T08:57:44] 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=7427135)
[2026-06-08T08:57:46] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7427135)
[2026-06-08T08:57:49] Filtering viral contigs with expression lower than the top 5 (remaining=7427135)
[2026-06-08T08:57:54] Filtering viral contigs with less than 5% coverage (remaining=7427135)
[2026-06-08T08:57:56] Estimating fragment length (mate gap mean=-87.0822, mate gap stddev=29.2208, read length mean=131.481)
[2026-06-08T08:57:57] Filtering read-through fragments with a distance <=10000bp (remaining=6932626)
[2026-06-08T08:57:59] Filtering inconsistently clipped mates (remaining=6822887)
[2026-06-08T08:58:01] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6694699)
[2026-06-08T08:58:06] Filtering fragments with small insert size (remaining=6693774)
[2026-06-08T08:58:08] Filtering alignments with long gaps (remaining=6693774)
[2026-06-08T08:58:11] Filtering fragments with both mates in the same gene (remaining=6692664)
[2026-06-08T08:58:13] Filtering fusions arising from hairpin structures (remaining=6341813)
[2026-06-08T08:58:16] Filtering reads with a mismatch p-value <=0.01 (remaining=2996311)
[2026-06-08T08:58:34] Filtering reads with low entropy (k-mer content >=60%) (remaining=1211240)
[2026-06-08T08:58:47] Finding fusions and counting supporting reads (total=877959)
[2026-06-08T08:59:06] Merging adjacent fusion breakpoints (remaining=866040)
[2026-06-08T08:59:08] Filtering multi-mapping fusions by alignment score and read support (remaining=574171)
[2026-06-08T08:59:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:57] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=572231)
[2026-06-08T08:59:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=327885)
[2026-06-08T08:59:59] Filtering fusions with <2 supporting reads (remaining=44937)
[2026-06-08T09:00:00] Filtering fusions with an e-value >=0.3 (remaining=12126)
[2026-06-08T09:00:01] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12190)
[2026-06-08T09:00:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12126)
[2026-06-08T09:00:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12126)
[2026-06-08T09:00:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8232)
[2026-06-08T09:00:15] Searching for fusions with spliced split reads (remaining=8271)
[2026-06-08T09:00:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=4329)
[2026-06-08T09:00:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4260)
[2026-06-08T09:00:23] Searching for fusions with >=4 spliced events (remaining=5586)
[2026-06-08T09:00:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2594)
[2026-06-08T09:00:40] Filtering fusions with anchors <=23nt (remaining=2167)
[2026-06-08T09:00:40] Filtering end-to-end fusions with low support (remaining=2103)
[2026-06-08T09:00:41] Filtering fusions with no coverage around the breakpoints (remaining=2065)
[2026-06-08T09:00:42] Indexing gene sequences 
[2026-06-08T09:00:48] Filtering genes with >=30% identity (remaining=524)
[2026-06-08T09:00:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=169)
[2026-06-08T09:00:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=155)
[2026-06-08T09:00:55] Searching for additional isoforms (remaining=207)
[2026-06-08T09:00:57] Assigning confidence scores to events 
[2026-06-08T09:01:01] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:01] Writing fusions to file 'tih_rna_sample_00649_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:01:03] Writing discarded fusions to file 'tih_rna_sample_00649_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:39] Freeing resources
[2026-06-08T09:01:58] Done (elapsed time=00:12:24, CPU time=00:12:23, peak memory=16.3gb)