[2026-06-08T08:22:41] Launching Arriba 2.4.0
[2026-06-08T08:22:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:22:58] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:23:03] Reading chimeric alignments from 'tih_rna_sample_00096_23H5VFLT4_s11.Aligned.sortedByCoord.out.bam' (total=9815076)
[2026-06-08T08:31:07] Marking multi-mapping alignments (marked=6395820)
[2026-06-08T08:31:12] Detecting strandedness (reverse)
[2026-06-08T08:31:12] Assigning strands to alignments 
[2026-06-08T08:31:14] Annotating alignments 
[2026-06-08T08:31:56] Filtering duplicates (remaining=6446718)
[2026-06-08T08:32:04] 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=6015563)
[2026-06-08T08:32:06] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6015563)
[2026-06-08T08:32:08] Filtering viral contigs with expression lower than the top 5 (remaining=6015563)
[2026-06-08T08:32:13] Filtering viral contigs with less than 5% coverage (remaining=6015563)
[2026-06-08T08:32:16] Estimating fragment length (mate gap mean=-87.5255, mate gap stddev=29.9931, read length mean=130.312)
[2026-06-08T08:32:16] Filtering read-through fragments with a distance <=10000bp (remaining=5588209)
[2026-06-08T08:32:18] Filtering inconsistently clipped mates (remaining=5457348)
[2026-06-08T08:32:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5077779)
[2026-06-08T08:32:26] Filtering fragments with small insert size (remaining=5076674)
[2026-06-08T08:32:28] Filtering alignments with long gaps (remaining=5076674)
[2026-06-08T08:32:31] Filtering fragments with both mates in the same gene (remaining=5075003)
[2026-06-08T08:32:33] Filtering fusions arising from hairpin structures (remaining=4612180)
[2026-06-08T08:32:36] Filtering reads with a mismatch p-value <=0.01 (remaining=1968406)
[2026-06-08T08:32:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=1233094)
[2026-06-08T08:33:01] Finding fusions and counting supporting reads (total=1057782)
[2026-06-08T08:33:22] Merging adjacent fusion breakpoints (remaining=1051110)
[2026-06-08T08:33:24] Filtering multi-mapping fusions by alignment score and read support (remaining=624164)
[2026-06-08T08:34:00] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:34:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=621479)
[2026-06-08T08:34:11] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=397965)
[2026-06-08T08:34:12] Filtering fusions with <2 supporting reads (remaining=29824)
[2026-06-08T08:34:13] Filtering fusions with an e-value >=0.3 (remaining=7810)
[2026-06-08T08:34:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7877)
[2026-06-08T08:34:18] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7637)
[2026-06-08T08:34:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7637)
[2026-06-08T08:34:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5846)
[2026-06-08T08:34:27] Searching for fusions with spliced split reads (remaining=5987)
[2026-06-08T08:34:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=3654)
[2026-06-08T08:34:36] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3606)
[2026-06-08T08:34:37] Searching for fusions with >=4 spliced events (remaining=4549)
[2026-06-08T08:34:38] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2070)
[2026-06-08T08:34:57] Filtering fusions with anchors <=23nt (remaining=1701)
[2026-06-08T08:34:58] Filtering end-to-end fusions with low support (remaining=1657)
[2026-06-08T08:34:59] Filtering fusions with no coverage around the breakpoints (remaining=1631)
[2026-06-08T08:34:59] Indexing gene sequences 
[2026-06-08T08:35:07] Filtering genes with >=30% identity (remaining=497)
[2026-06-08T08:35:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=223)
[2026-06-08T08:35:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=198)
[2026-06-08T08:35:21] Searching for additional isoforms (remaining=257)
[2026-06-08T08:35:24] Assigning confidence scores to events 
[2026-06-08T08:35:29] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:35:29] Writing fusions to file 'tih_rna_sample_00096_23H5VFLT4_s11.arriba.fusions.tsv' 
[2026-06-08T08:35:32] Writing discarded fusions to file 'tih_rna_sample_00096_23H5VFLT4_s11.arriba.fusions.discarded.tsv'
[2026-06-08T08:36:22] Freeing resources
[2026-06-08T08:36:45] Done (elapsed time=00:14:04, CPU time=00:14:03, peak memory=15.1gb)