[2026-06-08T08:27:03] Launching Arriba 2.4.0
[2026-06-08T08:27:03] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:27:16] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:20] Reading chimeric alignments from 'aih-tih-sc-3b54a2-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=8178353)
[2026-06-08T08:32:12] Marking multi-mapping alignments (marked=5378202)
[2026-06-08T08:32:15] Detecting strandedness (reverse)
[2026-06-08T08:32:15] Assigning strands to alignments 
[2026-06-08T08:32:16] Annotating alignments 
[2026-06-08T08:32:41] Filtering duplicates (remaining=4459607)
[2026-06-08T08:32:45] 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=4262264)
[2026-06-08T08:32:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4262264)
[2026-06-08T08:32:48] Filtering viral contigs with expression lower than the top 5 (remaining=4262264)
[2026-06-08T08:32:51] Filtering viral contigs with less than 5% coverage (remaining=4262264)
[2026-06-08T08:32:53] Estimating fragment length (mate gap mean=-84.94, mate gap stddev=26.5989, read length mean=122.676)
[2026-06-08T08:32:53] Filtering read-through fragments with a distance <=10000bp (remaining=3938782)
[2026-06-08T08:32:55] Filtering inconsistently clipped mates (remaining=3853137)
[2026-06-08T08:32:56] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3752538)
[2026-06-08T08:32:59] Filtering fragments with small insert size (remaining=3751800)
[2026-06-08T08:33:00] Filtering alignments with long gaps (remaining=3751800)
[2026-06-08T08:33:02] Filtering fragments with both mates in the same gene (remaining=3751036)
[2026-06-08T08:33:04] Filtering fusions arising from hairpin structures (remaining=3511597)
[2026-06-08T08:33:05] Filtering reads with a mismatch p-value <=0.01 (remaining=1506237)
[2026-06-08T08:33:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=739354)
[2026-06-08T08:33:21] Finding fusions and counting supporting reads (total=597677)
[2026-06-08T08:33:33] Merging adjacent fusion breakpoints (remaining=591943)
[2026-06-08T08:33:34] Filtering multi-mapping fusions by alignment score and read support (remaining=341242)
[2026-06-08T08:33:57] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:34:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=339969)
[2026-06-08T08:34:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=197475)
[2026-06-08T08:34:03] Filtering fusions with <2 supporting reads (remaining=22066)
[2026-06-08T08:34:03] Filtering fusions with an e-value >=0.3 (remaining=5167)
[2026-06-08T08:34:04] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5220)
[2026-06-08T08:34:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5149)
[2026-06-08T08:34:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5149)
[2026-06-08T08:34:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5057)
[2026-06-08T08:34:11] Searching for fusions with spliced split reads (remaining=5146)
[2026-06-08T08:34:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=3432)
[2026-06-08T08:34:15] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3405)
[2026-06-08T08:34:16] Searching for fusions with >=4 spliced events (remaining=4206)
[2026-06-08T08:34:17] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1936)
[2026-06-08T08:34:31] Filtering fusions with anchors <=23nt (remaining=1673)
[2026-06-08T08:34:31] Filtering end-to-end fusions with low support (remaining=1639)
[2026-06-08T08:34:32] Filtering fusions with no coverage around the breakpoints (remaining=1611)
[2026-06-08T08:34:32] Indexing gene sequences 
[2026-06-08T08:34:38] Filtering genes with >=30% identity (remaining=443)
[2026-06-08T08:34:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=136)
[2026-06-08T08:34:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=123)
[2026-06-08T08:34:43] Searching for additional isoforms (remaining=175)
[2026-06-08T08:34:44] Assigning confidence scores to events 
[2026-06-08T08:34:46] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:34:46] Writing fusions to file 'aih-tih-sc-3b54a2-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:34:48] Writing discarded fusions to file 'aih-tih-sc-3b54a2-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:35:10] Freeing resources
[2026-06-08T08:35:23] Done (elapsed time=00:08:20, CPU time=00:08:19, peak memory=12.8gb)