[2026-06-03T20:36:40] Launching Arriba 2.4.0
[2026-06-03T20:36:40] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:36:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:36:51] Reading chimeric alignments from 'aih-tih-sc-67e6e5-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=14739123)
[2026-06-03T20:43:39] Marking multi-mapping alignments (marked=10801447)
[2026-06-03T20:43:45] Detecting strandedness (reverse)
[2026-06-03T20:43:45] Assigning strands to alignments 
[2026-06-03T20:43:48] Annotating alignments 
[2026-06-03T20:44:32] Filtering duplicates (remaining=6864554)
[2026-06-03T20:44:40] 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=6036706)
[2026-06-03T20:44:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6036706)
[2026-06-03T20:44:46] Filtering viral contigs with expression lower than the top 5 (remaining=6036706)
[2026-06-03T20:44:52] Filtering viral contigs with less than 5% coverage (remaining=6036706)
[2026-06-03T20:44:55] Estimating fragment length (mate gap mean=-83.1743, mate gap stddev=29.8499, read length mean=121.406)
[2026-06-03T20:44:55] Filtering read-through fragments with a distance <=10000bp (remaining=5831716)
[2026-06-03T20:44:58] Filtering inconsistently clipped mates (remaining=5715909)
[2026-06-03T20:45:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5552055)
[2026-06-03T20:45:05] Filtering fragments with small insert size (remaining=5550482)
[2026-06-03T20:45:08] Filtering alignments with long gaps (remaining=5550482)
[2026-06-03T20:45:11] Filtering fragments with both mates in the same gene (remaining=5549254)
[2026-06-03T20:45:14] Filtering fusions arising from hairpin structures (remaining=5206209)
[2026-06-03T20:45:17] Filtering reads with a mismatch p-value <=0.01 (remaining=1775108)
[2026-06-03T20:45:30] Filtering reads with low entropy (k-mer content >=60%) (remaining=710623)
[2026-06-03T20:45:40] Finding fusions and counting supporting reads (total=577762)
[2026-06-03T20:45:59] Merging adjacent fusion breakpoints (remaining=569982)
[2026-06-03T20:46:01] Filtering multi-mapping fusions by alignment score and read support (remaining=323201)
[2026-06-03T20:46:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:46:51] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=320891)
[2026-06-03T20:46:52] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=203270)
[2026-06-03T20:46:53] Filtering fusions with <2 supporting reads (remaining=19974)
[2026-06-03T20:46:54] Filtering fusions with an e-value >=0.3 (remaining=5465)
[2026-06-03T20:46:55] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5517)
[2026-06-03T20:46:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5407)
[2026-06-03T20:47:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5407)
[2026-06-03T20:47:02] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4766)
[2026-06-03T20:47:08] Searching for fusions with spliced split reads (remaining=4865)
[2026-06-03T20:47:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=3268)
[2026-06-03T20:47:15] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3236)
[2026-06-03T20:47:16] Searching for fusions with >=4 spliced events (remaining=3672)
[2026-06-03T20:47:18] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1531)
[2026-06-03T20:47:34] Filtering fusions with anchors <=23nt (remaining=1017)
[2026-06-03T20:47:35] Filtering end-to-end fusions with low support (remaining=948)
[2026-06-03T20:47:36] Filtering fusions with no coverage around the breakpoints (remaining=925)
[2026-06-03T20:47:37] Indexing gene sequences 
[2026-06-03T20:47:42] Filtering genes with >=30% identity (remaining=345)
[2026-06-03T20:47:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=192)
[2026-06-03T20:47:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=170)
[2026-06-03T20:47:49] Searching for additional isoforms (remaining=218)
[2026-06-03T20:47:50] Assigning confidence scores to events 
[2026-06-03T20:47:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:47:54] Writing fusions to file 'aih-tih-sc-67e6e5-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:47:56] Writing discarded fusions to file 'aih-tih-sc-67e6e5-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:48:23] Freeing resources
[2026-06-03T20:48:45] Done (elapsed time=00:12:05, CPU time=00:12:04, peak memory=19.7gb)