[2026-06-08T08:34:36] Launching Arriba 2.4.0
[2026-06-08T08:34:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:34:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:34:48] Reading chimeric alignments from 'tih_rna_sample_00272_23H5VFLT4_s09.Aligned.sortedByCoord.out.bam' (total=9824077)
[2026-06-08T08:41:56] Marking multi-mapping alignments (marked=6334090)
[2026-06-08T08:42:00] Detecting strandedness (reverse)
[2026-06-08T08:42:00] Assigning strands to alignments 
[2026-06-08T08:42:02] Annotating alignments 
[2026-06-08T08:42:36] Filtering duplicates (remaining=6162980)
[2026-06-08T08:42:43] 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=5739344)
[2026-06-08T08:42:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5739344)
[2026-06-08T08:42:47] Filtering viral contigs with expression lower than the top 5 (remaining=5739344)
[2026-06-08T08:42:51] Filtering viral contigs with less than 5% coverage (remaining=5739344)
[2026-06-08T08:42:53] Estimating fragment length (mate gap mean=-88.3354, mate gap stddev=29.0385, read length mean=130.883)
[2026-06-08T08:42:53] Filtering read-through fragments with a distance <=10000bp (remaining=5339106)
[2026-06-08T08:42:55] Filtering inconsistently clipped mates (remaining=5216806)
[2026-06-08T08:42:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4859857)
[2026-06-08T08:43:02] Filtering fragments with small insert size (remaining=4858565)
[2026-06-08T08:43:04] Filtering alignments with long gaps (remaining=4858564)
[2026-06-08T08:43:06] Filtering fragments with both mates in the same gene (remaining=4856824)
[2026-06-08T08:43:08] Filtering fusions arising from hairpin structures (remaining=4398784)
[2026-06-08T08:43:10] Filtering reads with a mismatch p-value <=0.01 (remaining=1848795)
[2026-06-08T08:43:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=1157957)
[2026-06-08T08:43:33] Finding fusions and counting supporting reads (total=952865)
[2026-06-08T08:43:50] Merging adjacent fusion breakpoints (remaining=944900)
[2026-06-08T08:43:52] Filtering multi-mapping fusions by alignment score and read support (remaining=553822)
[2026-06-08T08:44:24] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:44:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=550880)
[2026-06-08T08:44:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=335459)
[2026-06-08T08:44:34] Filtering fusions with <2 supporting reads (remaining=32264)
[2026-06-08T08:44:35] Filtering fusions with an e-value >=0.3 (remaining=7963)
[2026-06-08T08:44:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8024)
[2026-06-08T08:44:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7796)
[2026-06-08T08:44:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7796)
[2026-06-08T08:44:42] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5965)
[2026-06-08T08:44:47] Searching for fusions with spliced split reads (remaining=6092)
[2026-06-08T08:44:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=3919)
[2026-06-08T08:44:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3862)
[2026-06-08T08:44:54] Searching for fusions with >=4 spliced events (remaining=4591)
[2026-06-08T08:44:55] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1801)
[2026-06-08T08:45:08] Filtering fusions with anchors <=23nt (remaining=1468)
[2026-06-08T08:45:09] Filtering end-to-end fusions with low support (remaining=1422)
[2026-06-08T08:45:10] Filtering fusions with no coverage around the breakpoints (remaining=1403)
[2026-06-08T08:45:11] Indexing gene sequences 
[2026-06-08T08:45:17] Filtering genes with >=30% identity (remaining=481)
[2026-06-08T08:45:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=224)
[2026-06-08T08:45:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=198)
[2026-06-08T08:45:29] Searching for additional isoforms (remaining=244)
[2026-06-08T08:45:30] Assigning confidence scores to events 
[2026-06-08T08:45:34] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:45:34] Writing fusions to file 'tih_rna_sample_00272_23H5VFLT4_s09.arriba.fusions.tsv' 
[2026-06-08T08:45:36] Writing discarded fusions to file 'tih_rna_sample_00272_23H5VFLT4_s09.arriba.fusions.discarded.tsv'
[2026-06-08T08:46:08] Freeing resources
[2026-06-08T08:46:26] Done (elapsed time=00:11:50, CPU time=00:11:49, peak memory=15gb)