[2026-05-28T21:20:35] Launching Arriba 2.4.0
[2026-05-28T21:20:35] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:20:51] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:20:57] Reading chimeric alignments from 'EndoN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=16050580)
[2026-05-28T21:32:38] Marking multi-mapping alignments (marked=11687610)
[2026-05-28T21:32:47] Detecting strandedness (reverse)
[2026-05-28T21:32:47] Assigning strands to alignments 
[2026-05-28T21:32:51] Annotating alignments 
[2026-05-28T21:34:22] Filtering duplicates (remaining=4958630)
[2026-05-28T21:34:37] 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=4437264)
[2026-05-28T21:34:42] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4437264)
[2026-05-28T21:34:45] Filtering viral contigs with expression lower than the top 5 (remaining=4437264)
[2026-05-28T21:34:53] Filtering viral contigs with less than 5% coverage (remaining=4437264)
[2026-05-28T21:34:58] Estimating fragment length (mate gap mean=-73.8963, mate gap stddev=28.2522, read length mean=109.337)
[2026-05-28T21:34:58] Filtering read-through fragments with a distance <=10000bp (remaining=4323980)
[2026-05-28T21:35:02] Filtering inconsistently clipped mates (remaining=4220498)
[2026-05-28T21:35:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3774398)
[2026-05-28T21:35:12] Filtering fragments with small insert size (remaining=3772096)
[2026-05-28T21:35:16] Filtering alignments with long gaps (remaining=3772096)
[2026-05-28T21:35:19] Filtering fragments with both mates in the same gene (remaining=3770811)
[2026-05-28T21:35:23] Filtering fusions arising from hairpin structures (remaining=3579117)
[2026-05-28T21:35:28] Filtering reads with a mismatch p-value <=0.01 (remaining=1153262)
[2026-05-28T21:35:38] Filtering reads with low entropy (k-mer content >=60%) (remaining=443612)
[2026-05-28T21:35:49] Finding fusions and counting supporting reads (total=419605)
[2026-05-28T21:36:20] Merging adjacent fusion breakpoints (remaining=416490)
[2026-05-28T21:36:22] Filtering multi-mapping fusions by alignment score and read support (remaining=184894)
[2026-05-28T21:37:39] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:37:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=182741)
[2026-05-28T21:37:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=135888)
[2026-05-28T21:37:52] Filtering fusions with <2 supporting reads (remaining=8125)
[2026-05-28T21:37:53] Filtering fusions with an e-value >=0.3 (remaining=1614)
[2026-05-28T21:37:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1628)
[2026-05-28T21:37:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1475)
[2026-05-28T21:38:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1475)
[2026-05-28T21:38:02] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1473)
[2026-05-28T21:38:11] Searching for fusions with spliced split reads (remaining=1590)
[2026-05-28T21:38:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=1251)
[2026-05-28T21:38:21] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1238)
[2026-05-28T21:38:22] Searching for fusions with >=4 spliced events (remaining=1313)
[2026-05-28T21:38:24] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=418)
[2026-05-28T21:38:53] Filtering fusions with anchors <=23nt (remaining=379)
[2026-05-28T21:38:54] Filtering end-to-end fusions with low support (remaining=365)
[2026-05-28T21:38:55] Filtering fusions with no coverage around the breakpoints (remaining=361)
[2026-05-28T21:38:56] Indexing gene sequences 
[2026-05-28T21:39:01] Filtering genes with >=30% identity (remaining=153)
[2026-05-28T21:39:02] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=78)
[2026-05-28T21:39:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=78)
[2026-05-28T21:39:06] Searching for additional isoforms (remaining=86)
[2026-05-28T21:39:07] Assigning confidence scores to events 
[2026-05-28T21:39:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:39:12] Writing fusions to file 'EndoN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:39:13] Writing discarded fusions to file 'EndoN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'