[2026-06-08T08:23:37] Launching Arriba 2.4.0
[2026-06-08T08:23:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:23:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:23:54] Reading chimeric alignments from 'tih_rna_sample_00377_23H5VFLT4_s23.Aligned.sortedByCoord.out.bam' (total=18186909)
[2026-06-08T08:32:21] Marking multi-mapping alignments (marked=12729365)
[2026-06-08T08:32:28] Detecting strandedness (reverse)
[2026-06-08T08:32:28] Assigning strands to alignments 
[2026-06-08T08:32:31] Annotating alignments 
[2026-06-08T08:33:31] Filtering duplicates (remaining=10754935)
[2026-06-08T08:33:43] 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=9781288)
[2026-06-08T08:33:46] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9781288)
[2026-06-08T08:33:49] Filtering viral contigs with expression lower than the top 5 (remaining=9781288)
[2026-06-08T08:33:57] Filtering viral contigs with less than 5% coverage (remaining=9781288)
[2026-06-08T08:34:00] Estimating fragment length (mate gap mean=-89.6313, mate gap stddev=31.0288, read length mean=128.396)
[2026-06-08T08:34:00] Filtering read-through fragments with a distance <=10000bp (remaining=9269173)
[2026-06-08T08:34:03] Filtering inconsistently clipped mates (remaining=9128559)
[2026-06-08T08:34:07] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=8786003)
[2026-06-08T08:34:15] Filtering fragments with small insert size (remaining=8783278)
[2026-06-08T08:34:18] Filtering alignments with long gaps (remaining=8783278)
[2026-06-08T08:34:22] Filtering fragments with both mates in the same gene (remaining=8781547)
[2026-06-08T08:34:25] Filtering fusions arising from hairpin structures (remaining=7979551)
[2026-06-08T08:34:29] Filtering reads with a mismatch p-value <=0.01 (remaining=2349242)
[2026-06-08T08:34:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=1658955)
[2026-06-08T08:35:03] Finding fusions and counting supporting reads (total=1352600)
[2026-06-08T08:35:31] Merging adjacent fusion breakpoints (remaining=1332666)
[2026-06-08T08:35:34] Filtering multi-mapping fusions by alignment score and read support (remaining=837055)
[2026-06-08T08:36:28] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:36:39] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=834920)
[2026-06-08T08:36:40] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=544162)
[2026-06-08T08:36:41] Filtering fusions with <2 supporting reads (remaining=39564)
[2026-06-08T08:36:42] Filtering fusions with an e-value >=0.3 (remaining=6648)
[2026-06-08T08:36:44] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6701)
[2026-06-08T08:36:50] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6539)
[2026-06-08T08:36:51] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6539)
[2026-06-08T08:36:53] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5486)
[2026-06-08T08:37:02] Searching for fusions with spliced split reads (remaining=5614)
[2026-06-08T08:37:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=4053)
[2026-06-08T08:37:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4023)
[2026-06-08T08:37:14] Searching for fusions with >=4 spliced events (remaining=4908)
[2026-06-08T08:37:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2421)
[2026-06-08T08:37:30] Filtering fusions with anchors <=23nt (remaining=1609)
[2026-06-08T08:37:32] Filtering end-to-end fusions with low support (remaining=1429)
[2026-06-08T08:37:33] Filtering fusions with no coverage around the breakpoints (remaining=1410)
[2026-06-08T08:37:34] Indexing gene sequences 
[2026-06-08T08:37:39] Filtering genes with >=30% identity (remaining=385)
[2026-06-08T08:37:42] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=192)
[2026-06-08T08:37:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=168)
[2026-06-08T08:37:50] Searching for additional isoforms (remaining=195)
[2026-06-08T08:37:53] Assigning confidence scores to events 
[2026-06-08T08:37:59] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:37:59] Writing fusions to file 'tih_rna_sample_00377_23H5VFLT4_s23.arriba.fusions.tsv' 
[2026-06-08T08:38:01] Writing discarded fusions to file 'tih_rna_sample_00377_23H5VFLT4_s23.arriba.fusions.discarded.tsv'
[2026-06-08T08:38:50] Freeing resources
[2026-06-08T08:39:20] Done (elapsed time=00:15:43, CPU time=00:15:42, peak memory=24.7gb)