[2026-06-08T08:37:29] Launching Arriba 2.4.0
[2026-06-08T08:37:29] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:37:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:37:45] Reading chimeric alignments from '1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=14188711)
[2026-06-08T08:44:32] Marking multi-mapping alignments (marked=9724962)
[2026-06-08T08:44:37] Detecting strandedness (reverse)
[2026-06-08T08:44:37] Assigning strands to alignments 
[2026-06-08T08:44:39] Annotating alignments 
[2026-06-08T08:45:23] Filtering duplicates (remaining=8164964)
[2026-06-08T08:45:32] 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=7658639)
[2026-06-08T08:45:35] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7658639)
[2026-06-08T08:45:38] Filtering viral contigs with expression lower than the top 5 (remaining=7658639)
[2026-06-08T08:45:44] Filtering viral contigs with less than 5% coverage (remaining=7658639)
[2026-06-08T08:45:47] Estimating fragment length (mate gap mean=-83.5689, mate gap stddev=27.4215, read length mean=123.516)
[2026-06-08T08:45:47] Filtering read-through fragments with a distance <=10000bp (remaining=7325272)
[2026-06-08T08:45:50] Filtering inconsistently clipped mates (remaining=7184883)
[2026-06-08T08:45:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7043408)
[2026-06-08T08:45:58] Filtering fragments with small insert size (remaining=7042032)
[2026-06-08T08:46:01] Filtering alignments with long gaps (remaining=7042032)
[2026-06-08T08:46:03] Filtering fragments with both mates in the same gene (remaining=7040792)
[2026-06-08T08:46:06] Filtering fusions arising from hairpin structures (remaining=6671146)
[2026-06-08T08:46:09] Filtering reads with a mismatch p-value <=0.01 (remaining=3059292)
[2026-06-08T08:46:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=1237630)
[2026-06-08T08:46:38] Finding fusions and counting supporting reads (total=1048020)
[2026-06-08T08:46:59] Merging adjacent fusion breakpoints (remaining=1039377)
[2026-06-08T08:47:01] Filtering multi-mapping fusions by alignment score and read support (remaining=576854)
[2026-06-08T08:47:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:47:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=575645)
[2026-06-08T08:47:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=432817)
[2026-06-08T08:47:58] Filtering fusions with <2 supporting reads (remaining=22592)
[2026-06-08T08:47:59] Filtering fusions with an e-value >=0.3 (remaining=4725)
[2026-06-08T08:48:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4818)
[2026-06-08T08:48:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4746)
[2026-06-08T08:48:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4748)
[2026-06-08T08:48:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4689)
[2026-06-08T08:48:14] Searching for fusions with spliced split reads (remaining=4779)
[2026-06-08T08:48:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=3490)
[2026-06-08T08:48:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3435)
[2026-06-08T08:48:23] Searching for fusions with >=4 spliced events (remaining=4015)
[2026-06-08T08:48:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1569)
[2026-06-08T08:48:40] Filtering fusions with anchors <=23nt (remaining=1255)
[2026-06-08T08:48:41] Filtering end-to-end fusions with low support (remaining=1201)
[2026-06-08T08:48:42] Filtering fusions with no coverage around the breakpoints (remaining=1159)
[2026-06-08T08:48:43] Indexing gene sequences 
[2026-06-08T08:48:48] Filtering genes with >=30% identity (remaining=353)
[2026-06-08T08:48:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=167)
[2026-06-08T08:48:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=159)
[2026-06-08T08:48:57] Searching for additional isoforms (remaining=205)
[2026-06-08T08:48:59] Assigning confidence scores to events 
[2026-06-08T08:49:03] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:49:03] Writing fusions to file '1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:49:05] Writing discarded fusions to file '1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:49:39] Freeing resources
[2026-06-08T08:49:59] Done (elapsed time=00:12:30, CPU time=00:12:29, peak memory=18.7gb)