[2026-06-08T08:31:04] Launching Arriba 2.4.0
[2026-06-08T08:31:04] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:31:19] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:31:23] Reading chimeric alignments from 'aih-tih-sc-51d534-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10246822)
[2026-06-08T08:39:00] Marking multi-mapping alignments (marked=6580447)
[2026-06-08T08:39:04] Detecting strandedness (reverse)
[2026-06-08T08:39:04] Assigning strands to alignments 
[2026-06-08T08:39:06] Annotating alignments 
[2026-06-08T08:39:38] Filtering duplicates (remaining=6449238)
[2026-06-08T08:39:48] 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=6217855)
[2026-06-08T08:39:55] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6217855)
[2026-06-08T08:39:59] Filtering viral contigs with expression lower than the top 5 (remaining=6217855)
[2026-06-08T08:40:03] Filtering viral contigs with less than 5% coverage (remaining=6217855)
[2026-06-08T08:40:05] Estimating fragment length (mate gap mean=-86.8996, mate gap stddev=28.4779, read length mean=133.342)
[2026-06-08T08:40:06] Filtering read-through fragments with a distance <=10000bp (remaining=5842817)
[2026-06-08T08:40:08] Filtering inconsistently clipped mates (remaining=5763038)
[2026-06-08T08:40:10] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5629593)
[2026-06-08T08:40:14] Filtering fragments with small insert size (remaining=5629036)
[2026-06-08T08:40:16] Filtering alignments with long gaps (remaining=5629035)
[2026-06-08T08:40:19] Filtering fragments with both mates in the same gene (remaining=5628220)
[2026-06-08T08:40:22] Filtering fusions arising from hairpin structures (remaining=5359913)
[2026-06-08T08:40:25] Filtering reads with a mismatch p-value <=0.01 (remaining=2721398)
[2026-06-08T08:40:40] Filtering reads with low entropy (k-mer content >=60%) (remaining=953059)
[2026-06-08T08:40:52] Finding fusions and counting supporting reads (total=690663)
[2026-06-08T08:41:08] Merging adjacent fusion breakpoints (remaining=682527)
[2026-06-08T08:41:10] Filtering multi-mapping fusions by alignment score and read support (remaining=427760)
[2026-06-08T08:41:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=425861)
[2026-06-08T08:41:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=240551)
[2026-06-08T08:41:50] Filtering fusions with <2 supporting reads (remaining=30839)
[2026-06-08T08:41:50] Filtering fusions with an e-value >=0.3 (remaining=8484)
[2026-06-08T08:41:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8526)
[2026-06-08T08:41:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8460)
[2026-06-08T08:41:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8460)
[2026-06-08T08:41:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6573)
[2026-06-08T08:42:01] Searching for fusions with spliced split reads (remaining=6666)
[2026-06-08T08:42:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=4368)
[2026-06-08T08:42:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4316)
[2026-06-08T08:42:08] Searching for fusions with >=4 spliced events (remaining=5035)
[2026-06-08T08:42:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1898)
[2026-06-08T08:42:29] Filtering fusions with anchors <=23nt (remaining=1504)
[2026-06-08T08:42:30] Filtering end-to-end fusions with low support (remaining=1465)
[2026-06-08T08:42:31] Filtering fusions with no coverage around the breakpoints (remaining=1429)
[2026-06-08T08:42:31] Indexing gene sequences 
[2026-06-08T08:42:38] Filtering genes with >=30% identity (remaining=450)
[2026-06-08T08:42:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=195)
[2026-06-08T08:42:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=178)
[2026-06-08T08:42:45] Searching for additional isoforms (remaining=227)
[2026-06-08T08:42:47] Assigning confidence scores to events 
[2026-06-08T08:42:50] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:42:50] Writing fusions to file 'aih-tih-sc-51d534-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:42:52] Writing discarded fusions to file 'aih-tih-sc-51d534-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:43:20] Freeing resources
[2026-06-08T08:43:37] Done (elapsed time=00:12:33, CPU time=00:12:32, peak memory=14.6gb)