[2026-06-08T08:49:24] Launching Arriba 2.4.0
[2026-06-08T08:49:24] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:40] Reading chimeric alignments from 'aih-tih-sc-67e6e5-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=14739123)
[2026-06-08T08:56:46] Marking multi-mapping alignments (marked=10801447)
[2026-06-08T08:56:52] Detecting strandedness (reverse)
[2026-06-08T08:56:52] Assigning strands to alignments 
[2026-06-08T08:56:55] Annotating alignments 
[2026-06-08T08:57:47] Filtering duplicates (remaining=6864554)
[2026-06-08T08:57:56] 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)
[2026-06-08T08:58:00] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6036706)
[2026-06-08T08:58:03] Filtering viral contigs with expression lower than the top 5 (remaining=6036706)
[2026-06-08T08:58:11] Filtering viral contigs with less than 5% coverage (remaining=6036706)
[2026-06-08T08:58:14] Estimating fragment length (mate gap mean=-83.1743, mate gap stddev=29.8499, read length mean=121.406)
[2026-06-08T08:58:14] Filtering read-through fragments with a distance <=10000bp (remaining=5831716)
[2026-06-08T08:58:18] Filtering inconsistently clipped mates (remaining=5715909)
[2026-06-08T08:58:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5552055)
[2026-06-08T08:58:27] Filtering fragments with small insert size (remaining=5550482)
[2026-06-08T08:58:31] Filtering alignments with long gaps (remaining=5550482)
[2026-06-08T08:58:34] Filtering fragments with both mates in the same gene (remaining=5549254)
[2026-06-08T08:58:37] Filtering fusions arising from hairpin structures (remaining=5206209)
[2026-06-08T08:58:41] Filtering reads with a mismatch p-value <=0.01 (remaining=1775108)
[2026-06-08T08:58:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=710623)
[2026-06-08T08:59:08] Finding fusions and counting supporting reads (total=577762)
[2026-06-08T08:59:29] Merging adjacent fusion breakpoints (remaining=569982)
[2026-06-08T08:59:30] Filtering multi-mapping fusions by alignment score and read support (remaining=323201)
[2026-06-08T09:00:12] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:19] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=320891)
[2026-06-08T09:00:20] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=203270)
[2026-06-08T09:00:21] Filtering fusions with <2 supporting reads (remaining=19974)
[2026-06-08T09:00:21] Filtering fusions with an e-value >=0.3 (remaining=5465)
[2026-06-08T09:00:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5517)
[2026-06-08T09:00:27] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5407)
[2026-06-08T09:00:28] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5407)
[2026-06-08T09:00:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4766)
[2026-06-08T09:00:35] Searching for fusions with spliced split reads (remaining=4865)
[2026-06-08T09:00:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=3268)
[2026-06-08T09:00:43] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3236)
[2026-06-08T09:00:44] Searching for fusions with >=4 spliced events (remaining=3672)
[2026-06-08T09:00:45] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1531)
[2026-06-08T09:01:06] Filtering fusions with anchors <=23nt (remaining=1017)
[2026-06-08T09:01:07] Filtering end-to-end fusions with low support (remaining=948)
[2026-06-08T09:01:07] Filtering fusions with no coverage around the breakpoints (remaining=925)
[2026-06-08T09:01:08] Indexing gene sequences 
[2026-06-08T09:01:14] Filtering genes with >=30% identity (remaining=345)
[2026-06-08T09:01:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=192)
[2026-06-08T09:01:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=170)
[2026-06-08T09:01:21] Searching for additional isoforms (remaining=218)
[2026-06-08T09:01:22] Assigning confidence scores to events 
[2026-06-08T09:01:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:26] Writing fusions to file 'aih-tih-sc-67e6e5-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:01:28] Writing discarded fusions to file 'aih-tih-sc-67e6e5-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:02:07] Freeing resources
[2026-06-08T09:02:33] Done (elapsed time=00:13:09, CPU time=00:13:08, peak memory=19.7gb)