[2026-06-08T08:38:11] Launching Arriba 2.4.0
[2026-06-08T08:38:11] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:38:19] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:38:23] Reading chimeric alignments from 'aih-tih-sc-6ff823-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10595867)
[2026-06-08T08:44:17] Marking multi-mapping alignments (marked=6833746)
[2026-06-08T08:44:21] Detecting strandedness (reverse)
[2026-06-08T08:44:21] Assigning strands to alignments 
[2026-06-08T08:44:23] Annotating alignments 
[2026-06-08T08:44:58] Filtering duplicates (remaining=4356965)
[2026-06-08T08:45:03] 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=4144771)
[2026-06-08T08:45:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4144771)
[2026-06-08T08:45:07] Filtering viral contigs with expression lower than the top 5 (remaining=4144771)
[2026-06-08T08:45:12] Filtering viral contigs with less than 5% coverage (remaining=4144771)
[2026-06-08T08:45:14] Estimating fragment length (mate gap mean=-86.1288, mate gap stddev=26.8545, read length mean=122.979)
[2026-06-08T08:45:14] Filtering read-through fragments with a distance <=10000bp (remaining=3849901)
[2026-06-08T08:45:16] Filtering inconsistently clipped mates (remaining=3772428)
[2026-06-08T08:45:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3673866)
[2026-06-08T08:45:22] Filtering fragments with small insert size (remaining=3672962)
[2026-06-08T08:45:24] Filtering alignments with long gaps (remaining=3672962)
[2026-06-08T08:45:26] Filtering fragments with both mates in the same gene (remaining=3672148)
[2026-06-08T08:45:28] Filtering fusions arising from hairpin structures (remaining=3465925)
[2026-06-08T08:45:30] Filtering reads with a mismatch p-value <=0.01 (remaining=1432648)
[2026-06-08T08:45:40] Filtering reads with low entropy (k-mer content >=60%) (remaining=664981)
[2026-06-08T08:45:48] Finding fusions and counting supporting reads (total=564938)
[2026-06-08T08:46:04] Merging adjacent fusion breakpoints (remaining=557063)
[2026-06-08T08:46:05] Filtering multi-mapping fusions by alignment score and read support (remaining=327480)
[2026-06-08T08:46:39] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:46:44] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=326344)
[2026-06-08T08:46:44] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=178039)
[2026-06-08T08:46:45] Filtering fusions with <2 supporting reads (remaining=20101)
[2026-06-08T08:46:46] Filtering fusions with an e-value >=0.3 (remaining=4436)
[2026-06-08T08:46:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4478)
[2026-06-08T08:46:50] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4408)
[2026-06-08T08:46:50] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4408)
[2026-06-08T08:46:51] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4350)
[2026-06-08T08:46:56] Searching for fusions with spliced split reads (remaining=4427)
[2026-06-08T08:47:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=3095)
[2026-06-08T08:47:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3062)
[2026-06-08T08:47:02] Searching for fusions with >=4 spliced events (remaining=3588)
[2026-06-08T08:47:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1423)
[2026-06-08T08:47:15] Filtering fusions with anchors <=23nt (remaining=1204)
[2026-06-08T08:47:16] Filtering end-to-end fusions with low support (remaining=1176)
[2026-06-08T08:47:16] Filtering fusions with no coverage around the breakpoints (remaining=1155)
[2026-06-08T08:47:17] Indexing gene sequences 
[2026-06-08T08:47:21] Filtering genes with >=30% identity (remaining=405)
[2026-06-08T08:47:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=205)
[2026-06-08T08:47:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=187)
[2026-06-08T08:47:25] Searching for additional isoforms (remaining=221)
[2026-06-08T08:47:27] Assigning confidence scores to events 
[2026-06-08T08:47:29] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:29] Writing fusions to file 'aih-tih-sc-6ff823-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:47:31] Writing discarded fusions to file 'aih-tih-sc-6ff823-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:54] Freeing resources
[2026-06-08T08:48:10] Done (elapsed time=00:09:59, CPU time=00:09:58, peak memory=15.2gb)