[2026-06-08T07:43:24] Launching Arriba 2.4.0
[2026-06-08T07:43:24] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:43:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:43:44] Reading chimeric alignments from 'EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=7590687)
[2026-06-08T07:46:53] Marking multi-mapping alignments (marked=5918498)
[2026-06-08T07:46:57] Detecting strandedness (reverse)
[2026-06-08T07:46:57] Assigning strands to alignments 
[2026-06-08T07:46:59] Annotating alignments 
[2026-06-08T07:47:32] Filtering duplicates (remaining=1868379)
[2026-06-08T07:47:37] 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=1519934)
[2026-06-08T07:47:39] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1519934)
[2026-06-08T07:47:41] Filtering viral contigs with expression lower than the top 5 (remaining=1519934)
[2026-06-08T07:47:44] Filtering viral contigs with less than 5% coverage (remaining=1519934)
[2026-06-08T07:47:46] Estimating fragment length (mate gap mean=-60.4535, mate gap stddev=27.3503, read length mean=94.0746)
[2026-06-08T07:47:46] Filtering read-through fragments with a distance <=10000bp (remaining=1486612)
[2026-06-08T07:47:48] Filtering inconsistently clipped mates (remaining=1441248)
[2026-06-08T07:47:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1305086)
[2026-06-08T07:47:52] Filtering fragments with small insert size (remaining=1303419)
[2026-06-08T07:47:54] Filtering alignments with long gaps (remaining=1303419)
[2026-06-08T07:47:55] Filtering fragments with both mates in the same gene (remaining=1302479)
[2026-06-08T07:47:57] Filtering fusions arising from hairpin structures (remaining=1238796)
[2026-06-08T07:47:59] Filtering reads with a mismatch p-value <=0.01 (remaining=227189)
[2026-06-08T07:48:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=92559)
[2026-06-08T07:48:07] Finding fusions and counting supporting reads (total=97457)
[2026-06-08T07:48:18] Merging adjacent fusion breakpoints (remaining=96800)
[2026-06-08T07:48:19] Filtering multi-mapping fusions by alignment score and read support (remaining=39591)
[2026-06-08T07:48:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:48:51] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=38783)
[2026-06-08T07:48:52] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=32832)
[2026-06-08T07:48:52] Filtering fusions with <2 supporting reads (remaining=729)
[2026-06-08T07:48:52] Filtering fusions with an e-value >=0.3 (remaining=184)
[2026-06-08T07:48:53] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=185)
[2026-06-08T07:48:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=153)
[2026-06-08T07:48:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=153)
[2026-06-08T07:48:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=144)
[2026-06-08T07:48:59] Searching for fusions with spliced split reads (remaining=151)
[2026-06-08T07:49:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=123)
[2026-06-08T07:49:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=120)
[2026-06-08T07:49:04] Searching for fusions with >=4 spliced events (remaining=120)
[2026-06-08T07:49:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=36)
[2026-06-08T07:49:22] Filtering fusions with anchors <=23nt (remaining=24)
[2026-06-08T07:49:22] Filtering end-to-end fusions with low support (remaining=24)
[2026-06-08T07:49:23] Filtering fusions with no coverage around the breakpoints (remaining=23)
[2026-06-08T07:49:23] Indexing gene sequences 
[2026-06-08T07:49:24] Filtering genes with >=30% identity (remaining=12)
[2026-06-08T07:49:24] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=1)
[2026-06-08T07:49:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=1)
[2026-06-08T07:49:25] Searching for additional isoforms (remaining=1)
[2026-06-08T07:49:26] Assigning confidence scores to events 
[2026-06-08T07:49:27] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:49:27] Writing fusions to file 'EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-06-08T07:49:28] Writing discarded fusions to file 'EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T07:49:42] Freeing resources
[2026-06-08T07:49:58] Done (elapsed time=00:06:34, CPU time=00:06:32, peak memory=11.7gb)