[2026-05-28T21:25:52] Launching Arriba 2.4.0
[2026-05-28T21:25:52] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:26:06] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:26:10] Reading chimeric alignments from 'MCF7_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam' (total=12544187)
[2026-05-28T21:34:44] Marking multi-mapping alignments (marked=8451534)
[2026-05-28T21:34:49] Detecting strandedness (reverse)
[2026-05-28T21:34:49] Assigning strands to alignments 
[2026-05-28T21:34:51] Annotating alignments 
[2026-05-28T21:35:32] Filtering duplicates (remaining=8988220)
[2026-05-28T21:35:41] 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)
[2026-05-28T21:35:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8291274)
[2026-05-28T21:35:46] Filtering viral contigs with expression lower than the top 5 (remaining=8291274)
[2026-05-28T21:35:52] Filtering viral contigs with less than 5% coverage (remaining=8291274)
[2026-05-28T21:35:54] Estimating fragment length (mate gap mean=-84.6105, mate gap stddev=30.0434, read length mean=129.711)
[2026-05-28T21:35:55] Filtering read-through fragments with a distance <=10000bp (remaining=7865667)
[2026-05-28T21:35:57] Filtering inconsistently clipped mates (remaining=7743761)
[2026-05-28T21:35:59] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7414626)
[2026-05-28T21:36:05] Filtering fragments with small insert size (remaining=7413283)
[2026-05-28T21:36:08] Filtering alignments with long gaps (remaining=7413282)
[2026-05-28T21:36:10] Filtering fragments with both mates in the same gene (remaining=7411762)
[2026-05-28T21:36:13] Filtering fusions arising from hairpin structures (remaining=7009717)
[2026-05-28T21:36:15] Filtering reads with a mismatch p-value <=0.01 (remaining=3434168)
[2026-05-28T21:36:35] Filtering reads with low entropy (k-mer content >=60%) (remaining=1554076)
[2026-05-28T21:36:50] Finding fusions and counting supporting reads (total=1175992)
[2026-05-28T21:37:11] Merging adjacent fusion breakpoints (remaining=1169285)
[2026-05-28T21:37:14] Filtering multi-mapping fusions by alignment score and read support (remaining=697277)
[2026-05-28T21:37:53] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:38:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=694288)
[2026-05-28T21:38:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=462353)
[2026-05-28T21:38:04] Filtering fusions with <2 supporting reads (remaining=43915)
[2026-05-28T21:38:05] Filtering fusions with an e-value >=0.3 (remaining=10278)
[2026-05-28T21:38:06] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10325)
[2026-05-28T21:38:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10027)
[2026-05-28T21:38:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10041)
[2026-05-28T21:38:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7947)
[2026-05-28T21:38:21] Searching for fusions with spliced split reads (remaining=8020)
[2026-05-28T21:38:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=4678)
[2026-05-28T21:38:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4633)
[2026-05-28T21:38:30] Searching for fusions with >=4 spliced events (remaining=6245)
[2026-05-28T21:38:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3070)
[2026-05-28T21:38:49] Filtering fusions with anchors <=23nt (remaining=2622)
[2026-05-28T21:38:50] Filtering end-to-end fusions with low support (remaining=2573)
[2026-05-28T21:38:51] Filtering fusions with no coverage around the breakpoints (remaining=2550)
[2026-05-28T21:38:52] Indexing gene sequences 
[2026-05-28T21:39:02] Filtering genes with >=30% identity (remaining=1193)
[2026-05-28T21:39:16] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=874)
[2026-05-28T21:39:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=440)
[2026-05-28T21:39:37] Searching for additional isoforms (remaining=691)
[2026-05-28T21:39:39] Assigning confidence scores to events 
[2026-05-28T21:39:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:39:44] Writing fusions to file 'MCF7_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv' 
[2026-05-28T21:39:53] Writing discarded fusions to file 'MCF7_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.discarded.tsv'
[2026-05-28T21:40:34] Freeing resources
[2026-05-28T21:40:55] Done (elapsed time=00:15:03, CPU time=00:15:02, peak memory=17.6gb)