[2026-05-28T20:29:32] Launching Arriba 2.4.0
[2026-05-28T20:29:32] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:29:46] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:29:51] Reading chimeric alignments from 'EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=7590687)
[2026-05-28T20:33:08] Marking multi-mapping alignments (marked=5918498)
[2026-05-28T20:33:11] Detecting strandedness (reverse)
[2026-05-28T20:33:11] Assigning strands to alignments 
[2026-05-28T20:33:13] Annotating alignments 
[2026-05-28T20:33:48] Filtering duplicates (remaining=1868379)
[2026-05-28T20:33:52] 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)
[2026-05-28T20:33:54] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1519934)
[2026-05-28T20:33:55] Filtering viral contigs with expression lower than the top 5 (remaining=1519934)
[2026-05-28T20:33:58] Filtering viral contigs with less than 5% coverage (remaining=1519934)
[2026-05-28T20:34:00] Estimating fragment length (mate gap mean=-60.4535, mate gap stddev=27.3503, read length mean=94.0746)
[2026-05-28T20:34:00] Filtering read-through fragments with a distance <=10000bp (remaining=1486612)
[2026-05-28T20:34:02] Filtering inconsistently clipped mates (remaining=1441248)
[2026-05-28T20:34:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1305086)
[2026-05-28T20:34:06] Filtering fragments with small insert size (remaining=1303419)
[2026-05-28T20:34:07] Filtering alignments with long gaps (remaining=1303419)
[2026-05-28T20:34:09] Filtering fragments with both mates in the same gene (remaining=1302479)
[2026-05-28T20:34:10] Filtering fusions arising from hairpin structures (remaining=1238796)
[2026-05-28T20:34:12] Filtering reads with a mismatch p-value <=0.01 (remaining=227189)
[2026-05-28T20:34:15] Filtering reads with low entropy (k-mer content >=60%) (remaining=92559)
[2026-05-28T20:34:19] Finding fusions and counting supporting reads (total=97457)
[2026-05-28T20:34:31] Merging adjacent fusion breakpoints (remaining=96800)
[2026-05-28T20:34:31] Filtering multi-mapping fusions by alignment score and read support (remaining=39591)
[2026-05-28T20:35:02] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:35:06] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=38783)
[2026-05-28T20:35:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=32832)
[2026-05-28T20:35:06] Filtering fusions with <2 supporting reads (remaining=729)
[2026-05-28T20:35:07] Filtering fusions with an e-value >=0.3 (remaining=184)
[2026-05-28T20:35:07] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=185)
[2026-05-28T20:35:09] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=153)
[2026-05-28T20:35:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=153)
[2026-05-28T20:35:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=144)
[2026-05-28T20:35:14] Searching for fusions with spliced split reads (remaining=151)
[2026-05-28T20:35:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=123)
[2026-05-28T20:35:19] Filtering read-through fusions with breakpoints near the gene boundary (remaining=120)
[2026-05-28T20:35:19] Searching for fusions with >=4 spliced events (remaining=120)
[2026-05-28T20:35:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=36)
[2026-05-28T20:35:39] Filtering fusions with anchors <=23nt (remaining=24)
[2026-05-28T20:35:39] Filtering end-to-end fusions with low support (remaining=24)
[2026-05-28T20:35:40] Filtering fusions with no coverage around the breakpoints (remaining=23)
[2026-05-28T20:35:40] Indexing gene sequences 
[2026-05-28T20:35:40] Filtering genes with >=30% identity (remaining=12)
[2026-05-28T20:35:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=1)
[2026-05-28T20:35:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=1)
[2026-05-28T20:35:42] Searching for additional isoforms (remaining=1)
[2026-05-28T20:35:42] Assigning confidence scores to events 
[2026-05-28T20:35:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:35:44] Writing fusions to file 'EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-05-28T20:35:45] Writing discarded fusions to file 'EndoN_FFPE_L02_RNA_01_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T20:35:58] Freeing resources
[2026-05-28T20:36:11] Done (elapsed time=00:06:39, CPU time=00:06:37, peak memory=11.8gb)