[2026-06-08T08:49:21] Launching Arriba 2.4.0
[2026-06-08T08:49:21] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:35] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:40] Reading chimeric alignments from 'aih-tih-sc-4fd42c-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10582587)
[2026-06-08T08:58:04] Marking multi-mapping alignments (marked=6922152)
[2026-06-08T08:58:09] Detecting strandedness (reverse)
[2026-06-08T08:58:09] Assigning strands to alignments 
[2026-06-08T08:58:12] Annotating alignments 
[2026-06-08T08:58:48] Filtering duplicates (remaining=6258171)
[2026-06-08T08:58:55] 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=5918350)
[2026-06-08T08:58:57] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5918350)
[2026-06-08T08:59:00] Filtering viral contigs with expression lower than the top 5 (remaining=5918350)
[2026-06-08T08:59:05] Filtering viral contigs with less than 5% coverage (remaining=5918350)
[2026-06-08T08:59:07] Estimating fragment length (mate gap mean=-86.3234, mate gap stddev=29.5695, read length mean=130.66)
[2026-06-08T08:59:08] Filtering read-through fragments with a distance <=10000bp (remaining=5537559)
[2026-06-08T08:59:10] Filtering inconsistently clipped mates (remaining=5445750)
[2026-06-08T08:59:12] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5322870)
[2026-06-08T08:59:17] Filtering fragments with small insert size (remaining=5322007)
[2026-06-08T08:59:20] Filtering alignments with long gaps (remaining=5322005)
[2026-06-08T08:59:22] Filtering fragments with both mates in the same gene (remaining=5321107)
[2026-06-08T08:59:24] Filtering fusions arising from hairpin structures (remaining=4985666)
[2026-06-08T08:59:27] Filtering reads with a mismatch p-value <=0.01 (remaining=2398229)
[2026-06-08T08:59:42] Filtering reads with low entropy (k-mer content >=60%) (remaining=1014093)
[2026-06-08T08:59:55] Finding fusions and counting supporting reads (total=780591)
[2026-06-08T09:00:12] Merging adjacent fusion breakpoints (remaining=770878)
[2026-06-08T09:00:13] Filtering multi-mapping fusions by alignment score and read support (remaining=506201)
[2026-06-08T09:00:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:52] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=504066)
[2026-06-08T09:00:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=266915)
[2026-06-08T09:00:54] Filtering fusions with <2 supporting reads (remaining=36206)
[2026-06-08T09:00:55] Filtering fusions with an e-value >=0.3 (remaining=10306)
[2026-06-08T09:00:55] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10372)
[2026-06-08T09:00:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10309)
[2026-06-08T09:01:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10309)
[2026-06-08T09:01:01] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7498)
[2026-06-08T09:01:06] Searching for fusions with spliced split reads (remaining=7506)
[2026-06-08T09:01:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=4638)
[2026-06-08T09:01:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4599)
[2026-06-08T09:01:13] Searching for fusions with >=4 spliced events (remaining=5677)
[2026-06-08T09:01:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2357)
[2026-06-08T09:01:31] Filtering fusions with anchors <=23nt (remaining=1867)
[2026-06-08T09:01:32] Filtering end-to-end fusions with low support (remaining=1822)
[2026-06-08T09:01:33] Filtering fusions with no coverage around the breakpoints (remaining=1782)
[2026-06-08T09:01:33] Indexing gene sequences 
[2026-06-08T09:01:40] Filtering genes with >=30% identity (remaining=592)
[2026-06-08T09:01:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=240)
[2026-06-08T09:01:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=186)
[2026-06-08T09:01:47] Searching for additional isoforms (remaining=259)
[2026-06-08T09:01:48] Assigning confidence scores to events 
[2026-06-08T09:01:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:52] Writing fusions to file 'aih-tih-sc-4fd42c-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:01:54] Writing discarded fusions to file 'aih-tih-sc-4fd42c-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:02:25] Freeing resources
[2026-06-08T09:02:42] Done (elapsed time=00:13:21, CPU time=00:13:20, peak memory=15.4gb)