[2026-06-08T08:36:37] Launching Arriba 2.4.0
[2026-06-08T08:36:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:36:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:36:52] Reading chimeric alignments from 'aih-tih-sc-28eb14-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9930373)
[2026-06-08T08:45:13] Marking multi-mapping alignments (marked=6540945)
[2026-06-08T08:45:20] Detecting strandedness (reverse)
[2026-06-08T08:45:20] Assigning strands to alignments 
[2026-06-08T08:45:23] Annotating alignments 
[2026-06-08T08:46:17] Filtering duplicates (remaining=6966669)
[2026-06-08T08:46:29] 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=6568950)
[2026-06-08T08:46:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6568950)
[2026-06-08T08:46:36] Filtering viral contigs with expression lower than the top 5 (remaining=6568950)
[2026-06-08T08:46:43] Filtering viral contigs with less than 5% coverage (remaining=6568950)
[2026-06-08T08:46:47] Estimating fragment length (mate gap mean=-85.8679, mate gap stddev=29.734, read length mean=132.778)
[2026-06-08T08:46:47] Filtering read-through fragments with a distance <=10000bp (remaining=6141646)
[2026-06-08T08:46:50] Filtering inconsistently clipped mates (remaining=6017887)
[2026-06-08T08:46:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5843125)
[2026-06-08T08:47:01] Filtering fragments with small insert size (remaining=5842272)
[2026-06-08T08:47:04] Filtering alignments with long gaps (remaining=5842271)
[2026-06-08T08:47:08] Filtering fragments with both mates in the same gene (remaining=5841127)
[2026-06-08T08:47:12] Filtering fusions arising from hairpin structures (remaining=5418047)
[2026-06-08T08:47:17] Filtering reads with a mismatch p-value <=0.01 (remaining=2460356)
[2026-06-08T08:47:37] Filtering reads with low entropy (k-mer content >=60%) (remaining=1191612)
[2026-06-08T08:47:53] Finding fusions and counting supporting reads (total=914558)
[2026-06-08T08:48:22] Merging adjacent fusion breakpoints (remaining=905493)
[2026-06-08T08:48:25] Filtering multi-mapping fusions by alignment score and read support (remaining=572763)
[2026-06-08T08:49:22] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:35] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=569454)
[2026-06-08T08:49:37] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=343643)
[2026-06-08T08:49:39] Filtering fusions with <2 supporting reads (remaining=35999)
[2026-06-08T08:49:40] Filtering fusions with an e-value >=0.3 (remaining=10952)
[2026-06-08T08:49:41] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11016)
[2026-06-08T08:49:48] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10936)
[2026-06-08T08:49:49] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10937)
[2026-06-08T08:49:52] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7661)
[2026-06-08T08:50:01] Searching for fusions with spliced split reads (remaining=7683)
[2026-06-08T08:50:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=4430)
[2026-06-08T08:50:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4373)
[2026-06-08T08:50:14] Searching for fusions with >=4 spliced events (remaining=5509)
[2026-06-08T08:50:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2605)
[2026-06-08T08:50:45] Filtering fusions with anchors <=23nt (remaining=2133)
[2026-06-08T08:50:46] Filtering end-to-end fusions with low support (remaining=2073)
[2026-06-08T08:50:47] Filtering fusions with no coverage around the breakpoints (remaining=2031)
[2026-06-08T08:50:49] Indexing gene sequences 
[2026-06-08T08:51:05] Filtering genes with >=30% identity (remaining=712)
[2026-06-08T08:51:16] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=374)
[2026-06-08T08:51:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=249)
[2026-06-08T08:51:33] Searching for additional isoforms (remaining=370)
[2026-06-08T08:51:36] Assigning confidence scores to events 
[2026-06-08T08:51:41] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:51:41] Writing fusions to file 'aih-tih-sc-28eb14-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:51:45] Writing discarded fusions to file 'aih-tih-sc-28eb14-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:52:43] Freeing resources
[2026-06-08T08:53:13] Done (elapsed time=00:16:36, CPU time=00:16:34, peak memory=14.7gb)