[2026-06-08T08:30:31] Launching Arriba 2.4.0
[2026-06-08T08:30:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:30:46] Reading chimeric alignments from 'MCF7_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam' (total=12544187)
[2026-06-08T08:38:57] Marking multi-mapping alignments (marked=8451534)
[2026-06-08T08:39:04] Detecting strandedness (reverse)
[2026-06-08T08:39:04] Assigning strands to alignments 
[2026-06-08T08:39:08] Annotating alignments 
[2026-06-08T08:40:10] Filtering duplicates (remaining=8988220)
[2026-06-08T08:40:23] 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=8291274)
[2026-06-08T08:40:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8291274)
[2026-06-08T08:40:30] Filtering viral contigs with expression lower than the top 5 (remaining=8291274)
[2026-06-08T08:40:39] Filtering viral contigs with less than 5% coverage (remaining=8291274)
[2026-06-08T08:40:43] Estimating fragment length (mate gap mean=-84.6105, mate gap stddev=30.0434, read length mean=129.711)
[2026-06-08T08:40:43] Filtering read-through fragments with a distance <=10000bp (remaining=7865667)
[2026-06-08T08:40:47] Filtering inconsistently clipped mates (remaining=7743761)
[2026-06-08T08:40:51] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7414626)
[2026-06-08T08:41:00] Filtering fragments with small insert size (remaining=7413283)
[2026-06-08T08:41:04] Filtering alignments with long gaps (remaining=7413282)
[2026-06-08T08:41:07] Filtering fragments with both mates in the same gene (remaining=7411762)
[2026-06-08T08:41:11] Filtering fusions arising from hairpin structures (remaining=7009717)
[2026-06-08T08:41:16] Filtering reads with a mismatch p-value <=0.01 (remaining=3434168)
[2026-06-08T08:41:37] Filtering reads with low entropy (k-mer content >=60%) (remaining=1554076)
[2026-06-08T08:41:56] Finding fusions and counting supporting reads (total=1175992)
[2026-06-08T08:42:30] Merging adjacent fusion breakpoints (remaining=1169285)
[2026-06-08T08:42:34] Filtering multi-mapping fusions by alignment score and read support (remaining=697277)
[2026-06-08T08:43:31] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:43:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=694288)
[2026-06-08T08:43:50] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=462353)
[2026-06-08T08:43:53] Filtering fusions with <2 supporting reads (remaining=43915)
[2026-06-08T08:43:54] Filtering fusions with an e-value >=0.3 (remaining=10278)
[2026-06-08T08:43:56] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10325)
[2026-06-08T08:44:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10027)
[2026-06-08T08:44:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10041)
[2026-06-08T08:44:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7947)
[2026-06-08T08:44:20] Searching for fusions with spliced split reads (remaining=8020)
[2026-06-08T08:44:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=4678)
[2026-06-08T08:44:34] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4633)
[2026-06-08T08:44:36] Searching for fusions with >=4 spliced events (remaining=6245)
[2026-06-08T08:44:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3070)
[2026-06-08T08:45:01] Filtering fusions with anchors <=23nt (remaining=2622)
[2026-06-08T08:45:02] Filtering end-to-end fusions with low support (remaining=2573)
[2026-06-08T08:45:04] Filtering fusions with no coverage around the breakpoints (remaining=2550)
[2026-06-08T08:45:06] Indexing gene sequences 
[2026-06-08T08:45:19] Filtering genes with >=30% identity (remaining=1193)
[2026-06-08T08:45:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=874)
[2026-06-08T08:46:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=440)
[2026-06-08T08:46:10] Searching for additional isoforms (remaining=691)
[2026-06-08T08:46:14] Assigning confidence scores to events 
[2026-06-08T08:46:23] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:46:24] Writing fusions to file 'MCF7_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:46:36] Writing discarded fusions to file 'MCF7_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:53] Freeing resources
[2026-06-08T08:48:39] Done (elapsed time=00:18:08, CPU time=00:18:06, peak memory=17.5gb)