[2026-06-08T08:43:28] Launching Arriba 2.4.0
[2026-06-08T08:43:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:43:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:43:43] Reading chimeric alignments from '1173_GFO_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=17684259)
[2026-06-08T08:50:48] Marking multi-mapping alignments (marked=12516570)
[2026-06-08T08:50:55] Detecting strandedness (no)
[2026-06-08T08:50:55] Annotating alignments 
[2026-06-08T08:51:51] Filtering duplicates (remaining=8338405)
[2026-06-08T08:52:02] 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=7598658)
[2026-06-08T08:52:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7598658)
[2026-06-08T08:52:08] Filtering viral contigs with expression lower than the top 5 (remaining=7598658)
[2026-06-08T08:52:16] Filtering viral contigs with less than 5% coverage (remaining=7598658)
[2026-06-08T08:52:19] Estimating fragment length (mate gap mean=-83.6485, mate gap stddev=27.6752, read length mean=122.496)
[2026-06-08T08:52:19] Filtering read-through fragments with a distance <=10000bp (remaining=7311626)
[2026-06-08T08:52:23] Filtering inconsistently clipped mates (remaining=7122487)
[2026-06-08T08:52:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6953109)
[2026-06-08T08:52:32] Filtering fragments with small insert size (remaining=6951477)
[2026-06-08T08:52:36] Filtering alignments with long gaps (remaining=6951476)
[2026-06-08T08:52:39] Filtering fragments with both mates in the same gene (remaining=6950261)
[2026-06-08T08:52:43] Filtering fusions arising from hairpin structures (remaining=6510503)
[2026-06-08T08:52:47] Filtering reads with a mismatch p-value <=0.01 (remaining=2795621)
[2026-06-08T08:53:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=1107597)
[2026-06-08T08:53:16] Finding fusions and counting supporting reads (total=971757)
[2026-06-08T08:53:39] Merging adjacent fusion breakpoints (remaining=961326)
[2026-06-08T08:53:41] Filtering multi-mapping fusions by alignment score and read support (remaining=494212)
[2026-06-08T08:54:33] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:54:42] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=493123)
[2026-06-08T08:54:42] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=378110)
[2026-06-08T08:54:44] Filtering fusions with <2 supporting reads (remaining=15437)
[2026-06-08T08:54:44] Filtering fusions with an e-value >=0.3 (remaining=3236)
[2026-06-08T08:54:45] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3362)
[2026-06-08T08:54:51] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3254)
[2026-06-08T08:54:52] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3254)
[2026-06-08T08:54:54] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3245)
[2026-06-08T08:55:02] Searching for fusions with spliced split reads (remaining=3299)
[2026-06-08T08:55:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=2432)
[2026-06-08T08:55:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2410)
[2026-06-08T08:55:12] Searching for fusions with >=4 spliced events (remaining=2746)
[2026-06-08T08:55:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1054)
[2026-06-08T08:55:28] Filtering fusions with anchors <=23nt (remaining=875)
[2026-06-08T08:55:28] Filtering end-to-end fusions with low support (remaining=845)
[2026-06-08T08:55:29] Filtering fusions with no coverage around the breakpoints (remaining=819)
[2026-06-08T08:55:30] Indexing gene sequences 
[2026-06-08T08:55:34] Filtering genes with >=30% identity (remaining=272)
[2026-06-08T08:55:36] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=120)
[2026-06-08T08:55:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=120)
[2026-06-08T08:55:41] Searching for additional isoforms (remaining=133)
[2026-06-08T08:55:42] Assigning confidence scores to events 
[2026-06-08T08:55:46] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:55:46] Writing fusions to file '1173_GFO_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:55:47] Writing discarded fusions to file '1173_GFO_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:56:21] Freeing resources
[2026-06-08T08:56:48] Done (elapsed time=00:13:20, CPU time=00:13:19, peak memory=22.2gb)