[2026-06-08T08:32:22] Launching Arriba 2.4.0
[2026-06-08T08:32:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:34] Reading chimeric alignments from 'aih-tih-sc-4dcd88-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11741567)
[2026-06-08T08:39:13] Marking multi-mapping alignments (marked=7442075)
[2026-06-08T08:39:17] Detecting strandedness (reverse)
[2026-06-08T08:39:17] Assigning strands to alignments 
[2026-06-08T08:39:19] Annotating alignments 
[2026-06-08T08:39:53] Filtering duplicates (remaining=7463120)
[2026-06-08T08:40:01] 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=7149336)
[2026-06-08T08:40:03] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7149336)
[2026-06-08T08:40:05] Filtering viral contigs with expression lower than the top 5 (remaining=7149336)
[2026-06-08T08:40:11] Filtering viral contigs with less than 5% coverage (remaining=7149336)
[2026-06-08T08:40:14] Estimating fragment length (mate gap mean=-86.8398, mate gap stddev=29.7992, read length mean=135.073)
[2026-06-08T08:40:14] Filtering read-through fragments with a distance <=10000bp (remaining=6773555)
[2026-06-08T08:40:16] Filtering inconsistently clipped mates (remaining=6685945)
[2026-06-08T08:40:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6526028)
[2026-06-08T08:40:22] Filtering fragments with small insert size (remaining=6525398)
[2026-06-08T08:40:24] Filtering alignments with long gaps (remaining=6525398)
[2026-06-08T08:40:27] Filtering fragments with both mates in the same gene (remaining=6524120)
[2026-06-08T08:40:29] Filtering fusions arising from hairpin structures (remaining=6270501)
[2026-06-08T08:40:32] Filtering reads with a mismatch p-value <=0.01 (remaining=3042098)
[2026-06-08T08:40:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=1023717)
[2026-06-08T08:40:56] Finding fusions and counting supporting reads (total=723188)
[2026-06-08T08:41:13] Merging adjacent fusion breakpoints (remaining=714547)
[2026-06-08T08:41:14] Filtering multi-mapping fusions by alignment score and read support (remaining=460177)
[2026-06-08T08:41:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=457647)
[2026-06-08T08:41:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=270068)
[2026-06-08T08:41:58] Filtering fusions with <2 supporting reads (remaining=37955)
[2026-06-08T08:41:59] Filtering fusions with an e-value >=0.3 (remaining=11914)
[2026-06-08T08:41:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11965)
[2026-06-08T08:42:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11838)
[2026-06-08T08:42:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11838)
[2026-06-08T08:42:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8681)
[2026-06-08T08:42:11] Searching for fusions with spliced split reads (remaining=8708)
[2026-06-08T08:42:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=5113)
[2026-06-08T08:42:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5045)
[2026-06-08T08:42:19] Searching for fusions with >=4 spliced events (remaining=5974)
[2026-06-08T08:42:21] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2091)
[2026-06-08T08:42:38] Filtering fusions with anchors <=23nt (remaining=1707)
[2026-06-08T08:42:39] Filtering end-to-end fusions with low support (remaining=1657)
[2026-06-08T08:42:40] Filtering fusions with no coverage around the breakpoints (remaining=1619)
[2026-06-08T08:42:41] Indexing gene sequences 
[2026-06-08T08:42:47] Filtering genes with >=30% identity (remaining=520)
[2026-06-08T08:42:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=283)
[2026-06-08T08:42:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=232)
[2026-06-08T08:42:57] Searching for additional isoforms (remaining=314)
[2026-06-08T08:42:59] Assigning confidence scores to events 
[2026-06-08T08:43:03] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:43:03] Writing fusions to file 'aih-tih-sc-4dcd88-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:43:05] Writing discarded fusions to file 'aih-tih-sc-4dcd88-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:43:34] Freeing resources
[2026-06-08T08:43:51] Done (elapsed time=00:11:29, CPU time=00:11:28, peak memory=16.1gb)