[2026-06-08T08:03:11] Launching Arriba 2.4.0
[2026-06-08T08:03:11] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:03:26] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:03:31] Reading chimeric alignments from 'tih_rna_sample_00703_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=7356564)
[2026-06-08T08:08:30] Marking multi-mapping alignments (marked=5060837)
[2026-06-08T08:08:34] Detecting strandedness (reverse)
[2026-06-08T08:08:34] Assigning strands to alignments 
[2026-06-08T08:08:35] Annotating alignments 
[2026-06-08T08:09:01] Filtering duplicates (remaining=2805725)
[2026-06-08T08:09:06] 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=2552776)
[2026-06-08T08:09:07] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2552776)
[2026-06-08T08:09:09] Filtering viral contigs with expression lower than the top 5 (remaining=2552776)
[2026-06-08T08:09:12] Filtering viral contigs with less than 5% coverage (remaining=2552776)
[2026-06-08T08:09:14] Estimating fragment length (mate gap mean=-86.4866, mate gap stddev=27.5241, read length mean=123.812)
[2026-06-08T08:09:14] Filtering read-through fragments with a distance <=10000bp (remaining=2455535)
[2026-06-08T08:09:16] Filtering inconsistently clipped mates (remaining=2399286)
[2026-06-08T08:09:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2331135)
[2026-06-08T08:09:20] Filtering fragments with small insert size (remaining=2330700)
[2026-06-08T08:09:22] Filtering alignments with long gaps (remaining=2330700)
[2026-06-08T08:09:24] Filtering fragments with both mates in the same gene (remaining=2330117)
[2026-06-08T08:09:26] Filtering fusions arising from hairpin structures (remaining=2175383)
[2026-06-08T08:09:27] Filtering reads with a mismatch p-value <=0.01 (remaining=907023)
[2026-06-08T08:09:35] Filtering reads with low entropy (k-mer content >=60%) (remaining=296056)
[2026-06-08T08:09:41] Finding fusions and counting supporting reads (total=248844)
[2026-06-08T08:09:51] Merging adjacent fusion breakpoints (remaining=246459)
[2026-06-08T08:09:52] Filtering multi-mapping fusions by alignment score and read support (remaining=138221)
[2026-06-08T08:10:15] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:10:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=137463)
[2026-06-08T08:10:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=80933)
[2026-06-08T08:10:19] Filtering fusions with <2 supporting reads (remaining=8638)
[2026-06-08T08:10:19] Filtering fusions with an e-value >=0.3 (remaining=2301)
[2026-06-08T08:10:19] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2339)
[2026-06-08T08:10:22] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2291)
[2026-06-08T08:10:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2291)
[2026-06-08T08:10:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2238)
[2026-06-08T08:10:26] Searching for fusions with spliced split reads (remaining=2353)
[2026-06-08T08:10:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=1769)
[2026-06-08T08:10:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1740)
[2026-06-08T08:10:30] Searching for fusions with >=4 spliced events (remaining=1881)
[2026-06-08T08:10:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=596)
[2026-06-08T08:10:45] Filtering fusions with anchors <=23nt (remaining=476)
[2026-06-08T08:10:45] Filtering end-to-end fusions with low support (remaining=454)
[2026-06-08T08:10:45] Filtering fusions with no coverage around the breakpoints (remaining=436)
[2026-06-08T08:10:46] Indexing gene sequences 
[2026-06-08T08:10:49] Filtering genes with >=30% identity (remaining=189)
[2026-06-08T08:10:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=137)
[2026-06-08T08:10:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=134)
[2026-06-08T08:10:53] Searching for additional isoforms (remaining=144)
[2026-06-08T08:10:53] Assigning confidence scores to events 
[2026-06-08T08:10:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:10:55] Writing fusions to file 'tih_rna_sample_00703_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:10:56] Writing discarded fusions to file 'tih_rna_sample_00703_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:11:12] Freeing resources
[2026-06-08T08:11:24] Done (elapsed time=00:08:13, CPU time=00:08:12, peak memory=11.7gb)