[2026-06-08T08:25:23] Launching Arriba 2.4.0
[2026-06-08T08:25:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:25:32] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:25:35] Reading chimeric alignments from 'tih_rna_sample_00754_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=9005012)
[2026-06-08T08:30:34] Marking multi-mapping alignments (marked=5754153)
[2026-06-08T08:30:38] Detecting strandedness (reverse)
[2026-06-08T08:30:38] Assigning strands to alignments 
[2026-06-08T08:30:39] Annotating alignments 
[2026-06-08T08:31:07] Filtering duplicates (remaining=5762961)
[2026-06-08T08:31:13] 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=5462322)
[2026-06-08T08:31:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5462322)
[2026-06-08T08:31:16] Filtering viral contigs with expression lower than the top 5 (remaining=5462322)
[2026-06-08T08:31:20] Filtering viral contigs with less than 5% coverage (remaining=5462322)
[2026-06-08T08:31:22] Estimating fragment length (mate gap mean=-87.5645, mate gap stddev=28.039, read length mean=131.239)
[2026-06-08T08:31:22] Filtering read-through fragments with a distance <=10000bp (remaining=5119667)
[2026-06-08T08:31:24] Filtering inconsistently clipped mates (remaining=5031354)
[2026-06-08T08:31:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4932048)
[2026-06-08T08:31:29] Filtering fragments with small insert size (remaining=4931373)
[2026-06-08T08:31:31] Filtering alignments with long gaps (remaining=4931373)
[2026-06-08T08:31:33] Filtering fragments with both mates in the same gene (remaining=4930575)
[2026-06-08T08:31:35] Filtering fusions arising from hairpin structures (remaining=4635273)
[2026-06-08T08:31:37] Filtering reads with a mismatch p-value <=0.01 (remaining=2270889)
[2026-06-08T08:31:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=823883)
[2026-06-08T08:31:58] Finding fusions and counting supporting reads (total=641073)
[2026-06-08T08:32:12] Merging adjacent fusion breakpoints (remaining=635596)
[2026-06-08T08:32:13] Filtering multi-mapping fusions by alignment score and read support (remaining=386672)
[2026-06-08T08:32:42] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:32:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=384648)
[2026-06-08T08:32:50] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=220830)
[2026-06-08T08:32:51] Filtering fusions with <2 supporting reads (remaining=27944)
[2026-06-08T08:32:51] Filtering fusions with an e-value >=0.3 (remaining=7077)
[2026-06-08T08:32:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7127)
[2026-06-08T08:32:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7048)
[2026-06-08T08:32:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7048)
[2026-06-08T08:32:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6304)
[2026-06-08T08:33:02] Searching for fusions with spliced split reads (remaining=6333)
[2026-06-08T08:33:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=4078)
[2026-06-08T08:33:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4008)
[2026-06-08T08:33:08] Searching for fusions with >=4 spliced events (remaining=4804)
[2026-06-08T08:33:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1872)
[2026-06-08T08:33:23] Filtering fusions with anchors <=23nt (remaining=1568)
[2026-06-08T08:33:23] Filtering end-to-end fusions with low support (remaining=1522)
[2026-06-08T08:33:24] Filtering fusions with no coverage around the breakpoints (remaining=1478)
[2026-06-08T08:33:24] Indexing gene sequences 
[2026-06-08T08:33:31] Filtering genes with >=30% identity (remaining=524)
[2026-06-08T08:33:34] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=313)
[2026-06-08T08:33:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=238)
[2026-06-08T08:33:40] Searching for additional isoforms (remaining=317)
[2026-06-08T08:33:41] Assigning confidence scores to events 
[2026-06-08T08:33:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:33:44] Writing fusions to file 'tih_rna_sample_00754_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:33:47] Writing discarded fusions to file 'tih_rna_sample_00754_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:34:14] Freeing resources
[2026-06-08T08:34:29] Done (elapsed time=00:09:06, CPU time=00:09:04, peak memory=13.6gb)