[2026-06-03T19:52:34] Launching Arriba 2.4.0
[2026-06-03T19:52:34] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:52:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:52:49] Reading chimeric alignments from 'aih-tih-sc-b567d0-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=7576450)
[2026-06-03T19:58:33] Marking multi-mapping alignments (marked=4911825)
[2026-06-03T19:58:36] Detecting strandedness (reverse)
[2026-06-03T19:58:36] Assigning strands to alignments 
[2026-06-03T19:58:38] Annotating alignments 
[2026-06-03T19:59:11] Filtering duplicates (remaining=5447051)
[2026-06-03T19:59:18] 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=5163577)
[2026-06-03T19:59:19] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5163577)
[2026-06-03T19:59:21] Filtering viral contigs with expression lower than the top 5 (remaining=5163577)
[2026-06-03T19:59:25] Filtering viral contigs with less than 5% coverage (remaining=5163577)
[2026-06-03T19:59:27] Estimating fragment length (mate gap mean=-85.4998, mate gap stddev=28.5952, read length mean=129.501)
[2026-06-03T19:59:27] Filtering read-through fragments with a distance <=10000bp (remaining=4868644)
[2026-06-03T19:59:29] Filtering inconsistently clipped mates (remaining=4769796)
[2026-06-03T19:59:30] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4640929)
[2026-06-03T19:59:34] Filtering fragments with small insert size (remaining=4640179)
[2026-06-03T19:59:35] Filtering alignments with long gaps (remaining=4640179)
[2026-06-03T19:59:37] Filtering fragments with both mates in the same gene (remaining=4639291)
[2026-06-03T19:59:39] Filtering fusions arising from hairpin structures (remaining=4317554)
[2026-06-03T19:59:41] Filtering reads with a mismatch p-value <=0.01 (remaining=1975865)
[2026-06-03T19:59:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=929020)
[2026-06-03T20:00:04] Finding fusions and counting supporting reads (total=741437)
[2026-06-03T20:00:22] Merging adjacent fusion breakpoints (remaining=736762)
[2026-06-03T20:00:24] Filtering multi-mapping fusions by alignment score and read support (remaining=466297)
[2026-06-03T20:00:58] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:01:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=464703)
[2026-06-03T20:01:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=295288)
[2026-06-03T20:01:07] Filtering fusions with <2 supporting reads (remaining=27919)
[2026-06-03T20:01:07] Filtering fusions with an e-value >=0.3 (remaining=6546)
[2026-06-03T20:01:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6603)
[2026-06-03T20:01:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6552)
[2026-06-03T20:01:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6552)
[2026-06-03T20:01:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5853)
[2026-06-03T20:01:20] Searching for fusions with spliced split reads (remaining=5969)
[2026-06-03T20:01:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=3879)
[2026-06-03T20:01:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3829)
[2026-06-03T20:01:29] Searching for fusions with >=4 spliced events (remaining=4617)
[2026-06-03T20:01:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1738)
[2026-06-03T20:01:49] Filtering fusions with anchors <=23nt (remaining=1409)
[2026-06-03T20:01:50] Filtering end-to-end fusions with low support (remaining=1367)
[2026-06-03T20:01:51] Filtering fusions with no coverage around the breakpoints (remaining=1332)
[2026-06-03T20:01:51] Indexing gene sequences 
[2026-06-03T20:01:58] Filtering genes with >=30% identity (remaining=358)
[2026-06-03T20:02:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=180)
[2026-06-03T20:02:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=161)
[2026-06-03T20:02:03] Searching for additional isoforms (remaining=210)
[2026-06-03T20:02:05] Assigning confidence scores to events 
[2026-06-03T20:02:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:02:08] Writing fusions to file 'aih-tih-sc-b567d0-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:02:10] Writing discarded fusions to file 'aih-tih-sc-b567d0-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:02:43] Freeing resources
[2026-06-03T20:02:57] Done (elapsed time=00:10:23, CPU time=00:10:22, peak memory=12.2gb)