[2026-06-08T08:17:22] Launching Arriba 2.4.0
[2026-06-08T08:17:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:17:32] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:17:36] Reading chimeric alignments from '1173_PCB_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=11599683)
[2026-06-08T08:23:05] Marking multi-mapping alignments (marked=7697724)
[2026-06-08T08:23:09] Detecting strandedness (reverse)
[2026-06-08T08:23:09] Assigning strands to alignments 
[2026-06-08T08:23:12] Annotating alignments 
[2026-06-08T08:23:50] Filtering duplicates (remaining=7755362)
[2026-06-08T08:23:58] 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=7418527)
[2026-06-08T08:24:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7418527)
[2026-06-08T08:24:03] Filtering viral contigs with expression lower than the top 5 (remaining=7418527)
[2026-06-08T08:24:08] Filtering viral contigs with less than 5% coverage (remaining=7418527)
[2026-06-08T08:24:11] Estimating fragment length (mate gap mean=-82.3168, mate gap stddev=26.8033, read length mean=122.042)
[2026-06-08T08:24:11] Filtering read-through fragments with a distance <=10000bp (remaining=7125290)
[2026-06-08T08:24:13] Filtering inconsistently clipped mates (remaining=6972621)
[2026-06-08T08:24:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6837735)
[2026-06-08T08:24:20] Filtering fragments with small insert size (remaining=6836561)
[2026-06-08T08:24:23] Filtering alignments with long gaps (remaining=6836560)
[2026-06-08T08:24:25] Filtering fragments with both mates in the same gene (remaining=6835424)
[2026-06-08T08:24:28] Filtering fusions arising from hairpin structures (remaining=6430389)
[2026-06-08T08:24:31] Filtering reads with a mismatch p-value <=0.01 (remaining=3033668)
[2026-06-08T08:24:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=1257098)
[2026-06-08T08:24:58] Finding fusions and counting supporting reads (total=1109283)
[2026-06-08T08:25:18] Merging adjacent fusion breakpoints (remaining=1101530)
[2026-06-08T08:25:21] Filtering multi-mapping fusions by alignment score and read support (remaining=636958)
[2026-06-08T08:25:59] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:26:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=635770)
[2026-06-08T08:26:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=495315)
[2026-06-08T08:26:10] Filtering fusions with <2 supporting reads (remaining=23307)
[2026-06-08T08:26:11] Filtering fusions with an e-value >=0.3 (remaining=4352)
[2026-06-08T08:26:12] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4446)
[2026-06-08T08:26:16] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4385)
[2026-06-08T08:26:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4386)
[2026-06-08T08:26:19] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4366)
[2026-06-08T08:26:26] Searching for fusions with spliced split reads (remaining=4464)
[2026-06-08T08:26:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=3176)
[2026-06-08T08:26:34] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3139)
[2026-06-08T08:26:35] Searching for fusions with >=4 spliced events (remaining=3830)
[2026-06-08T08:26:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1620)
[2026-06-08T08:26:50] Filtering fusions with anchors <=23nt (remaining=1369)
[2026-06-08T08:26:51] Filtering end-to-end fusions with low support (remaining=1335)
[2026-06-08T08:26:52] Filtering fusions with no coverage around the breakpoints (remaining=1317)
[2026-06-08T08:26:53] Indexing gene sequences 
[2026-06-08T08:26:58] Filtering genes with >=30% identity (remaining=391)
[2026-06-08T08:27:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=183)
[2026-06-08T08:27:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=180)
[2026-06-08T08:27:07] Searching for additional isoforms (remaining=214)
[2026-06-08T08:27:09] Assigning confidence scores to events 
[2026-06-08T08:27:14] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:27:14] Writing fusions to file '1173_PCB_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:27:16] Writing discarded fusions to file '1173_PCB_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:27:54] Freeing resources
[2026-06-08T08:28:14] Done (elapsed time=00:10:52, CPU time=00:10:50, peak memory=16.1gb)