[2026-06-08T08:51:41] Launching Arriba 2.4.0
[2026-06-08T08:51:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:51:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:51:55] Reading chimeric alignments from 'tih_rna_sample_00479_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9749463)
[2026-06-08T08:59:09] Marking multi-mapping alignments (marked=5958904)
[2026-06-08T08:59:15] Detecting strandedness (reverse)
[2026-06-08T08:59:15] Assigning strands to alignments 
[2026-06-08T08:59:17] Annotating alignments 
[2026-06-08T08:59:55] Filtering duplicates (remaining=4763190)
[2026-06-08T09:00:01] 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=4544362)
[2026-06-08T09:00:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4544362)
[2026-06-08T09:00:06] Filtering viral contigs with expression lower than the top 5 (remaining=4544362)
[2026-06-08T09:00:11] Filtering viral contigs with less than 5% coverage (remaining=4544362)
[2026-06-08T09:00:13] Estimating fragment length (mate gap mean=-88.7328, mate gap stddev=28.3183, read length mean=135.027)
[2026-06-08T09:00:13] Filtering read-through fragments with a distance <=10000bp (remaining=4240661)
[2026-06-08T09:00:15] Filtering inconsistently clipped mates (remaining=4177490)
[2026-06-08T09:00:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4070669)
[2026-06-08T09:00:22] Filtering fragments with small insert size (remaining=4069890)
[2026-06-08T09:00:24] Filtering alignments with long gaps (remaining=4069890)
[2026-06-08T09:00:26] Filtering fragments with both mates in the same gene (remaining=4069127)
[2026-06-08T09:00:28] Filtering fusions arising from hairpin structures (remaining=3884231)
[2026-06-08T09:00:31] Filtering reads with a mismatch p-value <=0.01 (remaining=1733574)
[2026-06-08T09:00:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=818107)
[2026-06-08T09:00:53] Finding fusions and counting supporting reads (total=636687)
[2026-06-08T09:01:11] Merging adjacent fusion breakpoints (remaining=631264)
[2026-06-08T09:01:13] Filtering multi-mapping fusions by alignment score and read support (remaining=396785)
[2026-06-08T09:01:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:01:54] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=393891)
[2026-06-08T09:01:55] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=208615)
[2026-06-08T09:01:57] Filtering fusions with <2 supporting reads (remaining=31162)
[2026-06-08T09:01:58] Filtering fusions with an e-value >=0.3 (remaining=8700)
[2026-06-08T09:01:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8738)
[2026-06-08T09:02:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8674)
[2026-06-08T09:02:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8674)
[2026-06-08T09:02:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6871)
[2026-06-08T09:02:14] Searching for fusions with spliced split reads (remaining=7001)
[2026-06-08T09:02:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=4408)
[2026-06-08T09:02:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4367)
[2026-06-08T09:02:24] Searching for fusions with >=4 spliced events (remaining=5304)
[2026-06-08T09:02:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2028)
[2026-06-08T09:02:41] Filtering fusions with anchors <=23nt (remaining=1748)
[2026-06-08T09:02:42] Filtering end-to-end fusions with low support (remaining=1718)
[2026-06-08T09:02:43] Filtering fusions with no coverage around the breakpoints (remaining=1683)
[2026-06-08T09:02:43] Indexing gene sequences 
[2026-06-08T09:02:54] Filtering genes with >=30% identity (remaining=672)
[2026-06-08T09:02:59] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=470)
[2026-06-08T09:03:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=336)
[2026-06-08T09:03:06] Searching for additional isoforms (remaining=472)
[2026-06-08T09:03:07] Assigning confidence scores to events 
[2026-06-08T09:03:10] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:03:10] Writing fusions to file 'tih_rna_sample_00479_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:03:14] Writing discarded fusions to file 'tih_rna_sample_00479_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:03:45] Freeing resources
[2026-06-08T09:04:06] Done (elapsed time=00:12:25, CPU time=00:12:23, peak memory=14.2gb)