[2026-06-08T08:19:24] Launching Arriba 2.4.0
[2026-06-08T08:19:24] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:19:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:19:46] Reading chimeric alignments from 'aih-tih-sc-992d78-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9826410)
[2026-06-08T08:27:24] Marking multi-mapping alignments (marked=6176425)
[2026-06-08T08:27:29] Detecting strandedness (reverse)
[2026-06-08T08:27:29] Assigning strands to alignments 
[2026-06-08T08:27:31] Annotating alignments 
[2026-06-08T08:28:10] Filtering duplicates (remaining=6339071)
[2026-06-08T08:28:18] 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=6029808)
[2026-06-08T08:28:20] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6029808)
[2026-06-08T08:28:23] Filtering viral contigs with expression lower than the top 5 (remaining=6029808)
[2026-06-08T08:28:28] Filtering viral contigs with less than 5% coverage (remaining=6029808)
[2026-06-08T08:28:30] Estimating fragment length (mate gap mean=-82.4683, mate gap stddev=28.4299, read length mean=123.626)
[2026-06-08T08:28:30] Filtering read-through fragments with a distance <=10000bp (remaining=5613894)
[2026-06-08T08:28:32] Filtering inconsistently clipped mates (remaining=5511624)
[2026-06-08T08:28:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5378237)
[2026-06-08T08:28:40] Filtering fragments with small insert size (remaining=5376979)
[2026-06-08T08:28:42] Filtering alignments with long gaps (remaining=5376979)
[2026-06-08T08:28:45] Filtering fragments with both mates in the same gene (remaining=5375702)
[2026-06-08T08:28:47] Filtering fusions arising from hairpin structures (remaining=5088931)
[2026-06-08T08:28:50] Filtering reads with a mismatch p-value <=0.01 (remaining=2292940)
[2026-06-08T08:29:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=1172690)
[2026-06-08T08:29:15] Finding fusions and counting supporting reads (total=881924)
[2026-06-08T08:29:35] Merging adjacent fusion breakpoints (remaining=875710)
[2026-06-08T08:29:37] Filtering multi-mapping fusions by alignment score and read support (remaining=548577)
[2026-06-08T08:30:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:30:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=547029)
[2026-06-08T08:30:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=322970)
[2026-06-08T08:30:20] Filtering fusions with <2 supporting reads (remaining=41444)
[2026-06-08T08:30:21] Filtering fusions with an e-value >=0.3 (remaining=9978)
[2026-06-08T08:30:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10017)
[2026-06-08T08:30:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9976)
[2026-06-08T08:30:27] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9976)
[2026-06-08T08:30:28] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8323)
[2026-06-08T08:30:34] Searching for fusions with spliced split reads (remaining=8452)
[2026-06-08T08:30:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=5329)
[2026-06-08T08:30:42] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5272)
[2026-06-08T08:30:43] Searching for fusions with >=4 spliced events (remaining=6461)
[2026-06-08T08:30:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2395)
[2026-06-08T08:31:04] Filtering fusions with anchors <=23nt (remaining=2040)
[2026-06-08T08:31:04] Filtering end-to-end fusions with low support (remaining=2005)
[2026-06-08T08:31:05] Filtering fusions with no coverage around the breakpoints (remaining=1971)
[2026-06-08T08:31:06] Indexing gene sequences 
[2026-06-08T08:31:15] Filtering genes with >=30% identity (remaining=589)
[2026-06-08T08:31:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=259)
[2026-06-08T08:31:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=222)
[2026-06-08T08:31:26] Searching for additional isoforms (remaining=283)
[2026-06-08T08:31:28] Assigning confidence scores to events 
[2026-06-08T08:31:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:31:34] Writing fusions to file 'aih-tih-sc-992d78-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:31:37] Writing discarded fusions to file 'aih-tih-sc-992d78-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:32:22] Freeing resources
[2026-06-08T08:32:42] Done (elapsed time=00:13:18, CPU time=00:13:17, peak memory=14.5gb)