[2026-06-08T08:49:34] Launching Arriba 2.4.0
[2026-06-08T08:49:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:50] Reading chimeric alignments from 'tih_rna_sample_00681_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11494876)
[2026-06-08T08:56:45] Marking multi-mapping alignments (marked=7167808)
[2026-06-08T08:56:50] Detecting strandedness (reverse)
[2026-06-08T08:56:50] Assigning strands to alignments 
[2026-06-08T08:56:52] Annotating alignments 
[2026-06-08T08:57:26] Filtering duplicates (remaining=7640169)
[2026-06-08T08:57:33] 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=7240425)
[2026-06-08T08:57:35] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7240425)
[2026-06-08T08:57:37] Filtering viral contigs with expression lower than the top 5 (remaining=7240425)
[2026-06-08T08:57:42] Filtering viral contigs with less than 5% coverage (remaining=7240425)
[2026-06-08T08:57:45] Estimating fragment length (mate gap mean=-87.3956, mate gap stddev=29.3617, read length mean=133.031)
[2026-06-08T08:57:45] Filtering read-through fragments with a distance <=10000bp (remaining=6761359)
[2026-06-08T08:57:47] Filtering inconsistently clipped mates (remaining=6656588)
[2026-06-08T08:57:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6517833)
[2026-06-08T08:57:54] Filtering fragments with small insert size (remaining=6516857)
[2026-06-08T08:57:56] Filtering alignments with long gaps (remaining=6516855)
[2026-06-08T08:57:59] Filtering fragments with both mates in the same gene (remaining=6515806)
[2026-06-08T08:58:01] Filtering fusions arising from hairpin structures (remaining=6117156)
[2026-06-08T08:58:03] Filtering reads with a mismatch p-value <=0.01 (remaining=2953542)
[2026-06-08T08:58:19] Filtering reads with low entropy (k-mer content >=60%) (remaining=1146993)
[2026-06-08T08:58:33] Finding fusions and counting supporting reads (total=855081)
[2026-06-08T08:58:50] Merging adjacent fusion breakpoints (remaining=844057)
[2026-06-08T08:58:52] Filtering multi-mapping fusions by alignment score and read support (remaining=558009)
[2026-06-08T08:59:24] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:31] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=555951)
[2026-06-08T08:59:32] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=304553)
[2026-06-08T08:59:33] Filtering fusions with <2 supporting reads (remaining=40889)
[2026-06-08T08:59:34] Filtering fusions with an e-value >=0.3 (remaining=11999)
[2026-06-08T08:59:35] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12055)
[2026-06-08T08:59:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11939)
[2026-06-08T08:59:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11939)
[2026-06-08T08:59:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8948)
[2026-06-08T08:59:47] Searching for fusions with spliced split reads (remaining=8968)
[2026-06-08T08:59:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=5228)
[2026-06-08T08:59:54] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5154)
[2026-06-08T08:59:55] Searching for fusions with >=4 spliced events (remaining=6247)
[2026-06-08T08:59:56] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2325)
[2026-06-08T09:00:14] Filtering fusions with anchors <=23nt (remaining=1782)
[2026-06-08T09:00:15] Filtering end-to-end fusions with low support (remaining=1718)
[2026-06-08T09:00:15] Filtering fusions with no coverage around the breakpoints (remaining=1677)
[2026-06-08T09:00:16] Indexing gene sequences 
[2026-06-08T09:00:21] Filtering genes with >=30% identity (remaining=487)
[2026-06-08T09:00:24] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=209)
[2026-06-08T09:00:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=188)
[2026-06-08T09:00:31] Searching for additional isoforms (remaining=232)
[2026-06-08T09:00:33] Assigning confidence scores to events 
[2026-06-08T09:00:36] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:36] Writing fusions to file 'tih_rna_sample_00681_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:00:39] Writing discarded fusions to file 'tih_rna_sample_00681_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:10] Freeing resources
[2026-06-08T09:01:28] Done (elapsed time=00:11:54, CPU time=00:11:53, peak memory=16.3gb)