[2026-06-08T08:37:33] Launching Arriba 2.4.0
[2026-06-08T08:37:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:37:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:37:46] Reading chimeric alignments from '1173_FWA_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=15173085)
[2026-06-08T08:45:03] Marking multi-mapping alignments (marked=10362117)
[2026-06-08T08:45:09] Detecting strandedness (reverse)
[2026-06-08T08:45:09] Assigning strands to alignments 
[2026-06-08T08:45:13] Annotating alignments 
[2026-06-08T08:46:02] Filtering duplicates (remaining=9655536)
[2026-06-08T08:46:12] 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=9033192)
[2026-06-08T08:46:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9033192)
[2026-06-08T08:46:18] Filtering viral contigs with expression lower than the top 5 (remaining=9033192)
[2026-06-08T08:46:24] Filtering viral contigs with less than 5% coverage (remaining=9033192)
[2026-06-08T08:46:27] Estimating fragment length (mate gap mean=-85.6057, mate gap stddev=27.7348, read length mean=127.553)
[2026-06-08T08:46:28] Filtering read-through fragments with a distance <=10000bp (remaining=8634524)
[2026-06-08T08:46:30] Filtering inconsistently clipped mates (remaining=8470256)
[2026-06-08T08:46:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=8317725)
[2026-06-08T08:46:39] Filtering fragments with small insert size (remaining=8316328)
[2026-06-08T08:46:41] Filtering alignments with long gaps (remaining=8316328)
[2026-06-08T08:46:44] Filtering fragments with both mates in the same gene (remaining=8315016)
[2026-06-08T08:46:47] Filtering fusions arising from hairpin structures (remaining=7848255)
[2026-06-08T08:46:51] Filtering reads with a mismatch p-value <=0.01 (remaining=3569866)
[2026-06-08T08:47:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=1295836)
[2026-06-08T08:47:24] Finding fusions and counting supporting reads (total=1123218)
[2026-06-08T08:47:49] Merging adjacent fusion breakpoints (remaining=1110824)
[2026-06-08T08:47:52] Filtering multi-mapping fusions by alignment score and read support (remaining=620184)
[2026-06-08T08:48:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:48:52] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=618555)
[2026-06-08T08:48:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=426853)
[2026-06-08T08:48:55] Filtering fusions with <2 supporting reads (remaining=26554)
[2026-06-08T08:48:56] Filtering fusions with an e-value >=0.3 (remaining=5100)
[2026-06-08T08:48:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5176)
[2026-06-08T08:49:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5079)
[2026-06-08T08:49:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5079)
[2026-06-08T08:49:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4967)
[2026-06-08T08:49:15] Searching for fusions with spliced split reads (remaining=5081)
[2026-06-08T08:49:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=3552)
[2026-06-08T08:49:25] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3522)
[2026-06-08T08:49:26] Searching for fusions with >=4 spliced events (remaining=4363)
[2026-06-08T08:49:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1958)
[2026-06-08T08:49:43] Filtering fusions with anchors <=23nt (remaining=1612)
[2026-06-08T08:49:44] Filtering end-to-end fusions with low support (remaining=1574)
[2026-06-08T08:49:45] Filtering fusions with no coverage around the breakpoints (remaining=1548)
[2026-06-08T08:49:46] Indexing gene sequences 
[2026-06-08T08:49:53] Filtering genes with >=30% identity (remaining=482)
[2026-06-08T08:49:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=211)
[2026-06-08T08:50:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=167)
[2026-06-08T08:50:03] Searching for additional isoforms (remaining=207)
[2026-06-08T08:50:06] Assigning confidence scores to events 
[2026-06-08T08:50:11] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:50:11] Writing fusions to file '1173_FWA_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:50:13] Writing discarded fusions to file '1173_FWA_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:56] Freeing resources
[2026-06-08T08:51:20] Done (elapsed time=00:13:47, CPU time=00:13:46, peak memory=19.7gb)