[2026-06-08T08:38:29] Launching Arriba 2.4.0
[2026-06-08T08:38:29] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:38:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:38:48] Reading chimeric alignments from 'aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9722572)
[2026-06-08T08:48:19] Marking multi-mapping alignments (marked=6253568)
[2026-06-08T08:48:26] Detecting strandedness (reverse)
[2026-06-08T08:48:26] Assigning strands to alignments 
[2026-06-08T08:48:29] Annotating alignments 
[2026-06-08T08:49:38] Filtering duplicates (remaining=6943727)
[2026-06-08T08:49:55] 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=6596321)
[2026-06-08T08:49:59] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6596321)
[2026-06-08T08:50:02] Filtering viral contigs with expression lower than the top 5 (remaining=6596321)
[2026-06-08T08:50:10] Filtering viral contigs with less than 5% coverage (remaining=6596321)
[2026-06-08T08:50:14] Estimating fragment length (mate gap mean=-85.9368, mate gap stddev=29.1834, read length mean=130.955)
[2026-06-08T08:50:14] Filtering read-through fragments with a distance <=10000bp (remaining=6197067)
[2026-06-08T08:50:17] Filtering inconsistently clipped mates (remaining=6060990)
[2026-06-08T08:50:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5884023)
[2026-06-08T08:50:28] Filtering fragments with small insert size (remaining=5883241)
[2026-06-08T08:50:32] Filtering alignments with long gaps (remaining=5883241)
[2026-06-08T08:50:35] Filtering fragments with both mates in the same gene (remaining=5882070)
[2026-06-08T08:50:39] Filtering fusions arising from hairpin structures (remaining=5455897)
[2026-06-08T08:50:43] Filtering reads with a mismatch p-value <=0.01 (remaining=2514743)
[2026-06-08T08:51:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=1289069)
[2026-06-08T08:51:16] Finding fusions and counting supporting reads (total=1016073)
[2026-06-08T08:51:44] Merging adjacent fusion breakpoints (remaining=1008224)
[2026-06-08T08:51:47] Filtering multi-mapping fusions by alignment score and read support (remaining=640363)
[2026-06-08T08:52:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:53:03] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=638630)
[2026-06-08T08:53:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=403200)
[2026-06-08T08:53:07] Filtering fusions with <2 supporting reads (remaining=35343)
[2026-06-08T08:53:08] Filtering fusions with an e-value >=0.3 (remaining=8249)
[2026-06-08T08:53:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8316)
[2026-06-08T08:53:16] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8213)
[2026-06-08T08:53:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8213)
[2026-06-08T08:53:20] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6935)
[2026-06-08T08:53:29] Searching for fusions with spliced split reads (remaining=6981)
[2026-06-08T08:53:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=4390)
[2026-06-08T08:53:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4344)
[2026-06-08T08:53:42] Searching for fusions with >=4 spliced events (remaining=5580)
[2026-06-08T08:53:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2724)
[2026-06-08T08:54:13] Filtering fusions with anchors <=23nt (remaining=2308)
[2026-06-08T08:54:15] Filtering end-to-end fusions with low support (remaining=2248)
[2026-06-08T08:54:16] Filtering fusions with no coverage around the breakpoints (remaining=2207)
[2026-06-08T08:54:17] Indexing gene sequences 
[2026-06-08T08:54:29] Filtering genes with >=30% identity (remaining=838)
[2026-06-08T08:54:49] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=529)
[2026-06-08T08:55:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=324)
[2026-06-08T08:55:03] Searching for additional isoforms (remaining=456)
[2026-06-08T08:55:05] Assigning confidence scores to events 
[2026-06-08T08:55:11] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:55:12] Writing fusions to file 'aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:55:18] Writing discarded fusions to file 'aih-tih-sc-f6bb6f-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:56:16] Freeing resources
[2026-06-08T08:56:54] Done (elapsed time=00:18:25, CPU time=00:18:23, peak memory=14.6gb)