[2026-06-08T08:26:36] Launching Arriba 2.4.0
[2026-06-08T08:26:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:26:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:26:55] Reading chimeric alignments from 'tih_rna_sample_00400_23H5VFLT4_s27.Aligned.sortedByCoord.out.bam' (total=10845429)
[2026-06-08T08:34:34] Marking multi-mapping alignments (marked=7247629)
[2026-06-08T08:34:39] Detecting strandedness (reverse)
[2026-06-08T08:34:39] Assigning strands to alignments 
[2026-06-08T08:34:41] Annotating alignments 
[2026-06-08T08:35:15] Filtering duplicates (remaining=6755356)
[2026-06-08T08:35:23] 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=6356083)
[2026-06-08T08:35:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6356083)
[2026-06-08T08:35:27] Filtering viral contigs with expression lower than the top 5 (remaining=6356083)
[2026-06-08T08:35:32] Filtering viral contigs with less than 5% coverage (remaining=6356083)
[2026-06-08T08:35:34] Estimating fragment length (mate gap mean=-84.3742, mate gap stddev=29.6014, read length mean=123.886)
[2026-06-08T08:35:34] Filtering read-through fragments with a distance <=10000bp (remaining=5794728)
[2026-06-08T08:35:37] Filtering inconsistently clipped mates (remaining=5646804)
[2026-06-08T08:35:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5328420)
[2026-06-08T08:35:44] Filtering fragments with small insert size (remaining=5326948)
[2026-06-08T08:35:46] Filtering alignments with long gaps (remaining=5326948)
[2026-06-08T08:35:48] Filtering fragments with both mates in the same gene (remaining=5325510)
[2026-06-08T08:35:51] Filtering fusions arising from hairpin structures (remaining=4880733)
[2026-06-08T08:35:53] Filtering reads with a mismatch p-value <=0.01 (remaining=2047077)
[2026-06-08T08:36:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=1358248)
[2026-06-08T08:36:17] Finding fusions and counting supporting reads (total=1091156)
[2026-06-08T08:36:35] Merging adjacent fusion breakpoints (remaining=1079490)
[2026-06-08T08:36:37] Filtering multi-mapping fusions by alignment score and read support (remaining=627988)
[2026-06-08T08:37:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:37:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=626155)
[2026-06-08T08:37:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=391922)
[2026-06-08T08:37:18] Filtering fusions with <2 supporting reads (remaining=33906)
[2026-06-08T08:37:19] Filtering fusions with an e-value >=0.3 (remaining=6768)
[2026-06-08T08:37:20] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6846)
[2026-06-08T08:37:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6690)
[2026-06-08T08:37:24] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6690)
[2026-06-08T08:37:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6043)
[2026-06-08T08:37:31] Searching for fusions with spliced split reads (remaining=6068)
[2026-06-08T08:37:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=4027)
[2026-06-08T08:37:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3967)
[2026-06-08T08:37:39] Searching for fusions with >=4 spliced events (remaining=4984)
[2026-06-08T08:37:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2129)
[2026-06-08T08:37:58] Filtering fusions with anchors <=23nt (remaining=1722)
[2026-06-08T08:37:59] Filtering end-to-end fusions with low support (remaining=1691)
[2026-06-08T08:37:59] Filtering fusions with no coverage around the breakpoints (remaining=1673)
[2026-06-08T08:38:00] Indexing gene sequences 
[2026-06-08T08:38:06] Filtering genes with >=30% identity (remaining=477)
[2026-06-08T08:38:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=210)
[2026-06-08T08:38:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=183)
[2026-06-08T08:38:15] Searching for additional isoforms (remaining=229)
[2026-06-08T08:38:16] Assigning confidence scores to events 
[2026-06-08T08:38:20] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:38:20] Writing fusions to file 'tih_rna_sample_00400_23H5VFLT4_s27.arriba.fusions.tsv' 
[2026-06-08T08:38:22] Writing discarded fusions to file 'tih_rna_sample_00400_23H5VFLT4_s27.arriba.fusions.discarded.tsv'
[2026-06-08T08:38:55] Freeing resources
[2026-06-08T08:39:14] Done (elapsed time=00:12:38, CPU time=00:12:37, peak memory=16.1gb)