[2026-06-08T08:25:36] Launching Arriba 2.4.0
[2026-06-08T08:25:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:25:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:25:55] Reading chimeric alignments from '1173_NFO_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=16192517)
[2026-06-08T08:31:46] Marking multi-mapping alignments (marked=12074762)
[2026-06-08T08:31:52] Detecting strandedness (no)
[2026-06-08T08:31:52] Annotating alignments 
[2026-06-08T08:32:41] Filtering duplicates (remaining=5076881)
[2026-06-08T08:32:48] 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=4513444)
[2026-06-08T08:32:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4513444)
[2026-06-08T08:32:54] Filtering viral contigs with expression lower than the top 5 (remaining=4513444)
[2026-06-08T08:33:00] Filtering viral contigs with less than 5% coverage (remaining=4513444)
[2026-06-08T08:33:03] Estimating fragment length (mate gap mean=-74.8392, mate gap stddev=27.5283, read length mean=110.946)
[2026-06-08T08:33:03] Filtering read-through fragments with a distance <=10000bp (remaining=4413957)
[2026-06-08T08:33:06] Filtering inconsistently clipped mates (remaining=4287899)
[2026-06-08T08:33:09] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4187658)
[2026-06-08T08:33:13] Filtering fragments with small insert size (remaining=4185284)
[2026-06-08T08:33:16] Filtering alignments with long gaps (remaining=4185284)
[2026-06-08T08:33:18] Filtering fragments with both mates in the same gene (remaining=4184215)
[2026-06-08T08:33:21] Filtering fusions arising from hairpin structures (remaining=3901881)
[2026-06-08T08:33:24] Filtering reads with a mismatch p-value <=0.01 (remaining=1555250)
[2026-06-08T08:33:34] Filtering reads with low entropy (k-mer content >=60%) (remaining=450295)
[2026-06-08T08:33:44] Finding fusions and counting supporting reads (total=391338)
[2026-06-08T08:34:00] Merging adjacent fusion breakpoints (remaining=387630)
[2026-06-08T08:34:01] Filtering multi-mapping fusions by alignment score and read support (remaining=195170)
[2026-06-08T08:34:42] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:34:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=194245)
[2026-06-08T08:34:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=131650)
[2026-06-08T08:34:48] Filtering fusions with <2 supporting reads (remaining=7396)
[2026-06-08T08:34:49] Filtering fusions with an e-value >=0.3 (remaining=1899)
[2026-06-08T08:34:49] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2026)
[2026-06-08T08:34:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1952)
[2026-06-08T08:34:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1952)
[2026-06-08T08:34:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1951)
[2026-06-08T08:35:00] Searching for fusions with spliced split reads (remaining=2053)
[2026-06-08T08:35:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=1523)
[2026-06-08T08:35:06] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1505)
[2026-06-08T08:35:07] Searching for fusions with >=4 spliced events (remaining=1634)
[2026-06-08T08:35:08] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=666)
[2026-06-08T08:35:21] Filtering fusions with anchors <=23nt (remaining=593)
[2026-06-08T08:35:22] Filtering end-to-end fusions with low support (remaining=540)
[2026-06-08T08:35:22] Filtering fusions with no coverage around the breakpoints (remaining=505)
[2026-06-08T08:35:23] Indexing gene sequences 
[2026-06-08T08:35:26] Filtering genes with >=30% identity (remaining=163)
[2026-06-08T08:35:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=83)
[2026-06-08T08:35:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=81)
[2026-06-08T08:35:29] Searching for additional isoforms (remaining=92)
[2026-06-08T08:35:30] Assigning confidence scores to events 
[2026-06-08T08:35:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:35:33] Writing fusions to file '1173_NFO_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:35:34] Writing discarded fusions to file '1173_NFO_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:35:53] Freeing resources
[2026-06-08T08:36:14] Done (elapsed time=00:10:38, CPU time=00:10:37, peak memory=20gb)