[2026-06-08T09:00:18] Launching Arriba 2.4.0
[2026-06-08T09:00:18] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:00:28] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:00:32] Reading chimeric alignments from 'aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10060417)
[2026-06-08T09:07:36] Marking multi-mapping alignments (marked=6266068)
[2026-06-08T09:07:41] Detecting strandedness (reverse)
[2026-06-08T09:07:41] Assigning strands to alignments 
[2026-06-08T09:07:43] Annotating alignments 
[2026-06-08T09:08:16] Filtering duplicates (remaining=5048490)
[2026-06-08T09:08:22] 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=4847806)
[2026-06-08T09:08:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4847806)
[2026-06-08T09:08:26] Filtering viral contigs with expression lower than the top 5 (remaining=4847806)
[2026-06-08T09:08:30] Filtering viral contigs with less than 5% coverage (remaining=4847806)
[2026-06-08T09:08:33] Estimating fragment length (mate gap mean=-85.8575, mate gap stddev=29.1914, read length mean=132.493)
[2026-06-08T09:08:33] Filtering read-through fragments with a distance <=10000bp (remaining=4569825)
[2026-06-08T09:08:35] Filtering inconsistently clipped mates (remaining=4490736)
[2026-06-08T09:08:37] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4352114)
[2026-06-08T09:08:41] Filtering fragments with small insert size (remaining=4351282)
[2026-06-08T09:08:43] Filtering alignments with long gaps (remaining=4351282)
[2026-06-08T09:08:45] Filtering fragments with both mates in the same gene (remaining=4350451)
[2026-06-08T09:08:47] Filtering fusions arising from hairpin structures (remaining=4098724)
[2026-06-08T09:08:50] Filtering reads with a mismatch p-value <=0.01 (remaining=1945974)
[2026-06-08T09:09:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=708357)
[2026-06-08T09:09:10] Finding fusions and counting supporting reads (total=561767)
[2026-06-08T09:09:26] Merging adjacent fusion breakpoints (remaining=556253)
[2026-06-08T09:09:27] Filtering multi-mapping fusions by alignment score and read support (remaining=358168)
[2026-06-08T09:10:00] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:10:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=355613)
[2026-06-08T09:10:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=185922)
[2026-06-08T09:10:07] Filtering fusions with <2 supporting reads (remaining=24984)
[2026-06-08T09:10:08] Filtering fusions with an e-value >=0.3 (remaining=7321)
[2026-06-08T09:10:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7364)
[2026-06-08T09:10:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7295)
[2026-06-08T09:10:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7295)
[2026-06-08T09:10:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5443)
[2026-06-08T09:10:18] Searching for fusions with spliced split reads (remaining=5528)
[2026-06-08T09:10:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=3566)
[2026-06-08T09:10:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3524)
[2026-06-08T09:10:24] Searching for fusions with >=4 spliced events (remaining=4080)
[2026-06-08T09:10:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1335)
[2026-06-08T09:10:39] Filtering fusions with anchors <=23nt (remaining=1074)
[2026-06-08T09:10:40] Filtering end-to-end fusions with low support (remaining=1048)
[2026-06-08T09:10:40] Filtering fusions with no coverage around the breakpoints (remaining=1026)
[2026-06-08T09:10:41] Indexing gene sequences 
[2026-06-08T09:10:45] Filtering genes with >=30% identity (remaining=362)
[2026-06-08T09:10:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=164)
[2026-06-08T09:10:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=138)
[2026-06-08T09:10:50] Searching for additional isoforms (remaining=176)
[2026-06-08T09:10:51] Assigning confidence scores to events 
[2026-06-08T09:10:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:10:54] Writing fusions to file 'aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:10:56] Writing discarded fusions to file 'aih-tih-sc-38a0a3-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:11:21] Freeing resources
[2026-06-08T09:11:38] Done (elapsed time=00:11:20, CPU time=00:11:18, peak memory=14.4gb)