[2026-06-08T07:37:57] Launching Arriba 2.4.0
[2026-06-08T07:37:57] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:38:09] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:38:14] Reading chimeric alignments from '1173_LAF_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=14157163)
[2026-06-08T07:42:20] Marking multi-mapping alignments (marked=12722585)
[2026-06-08T07:42:25] Detecting strandedness (no)
[2026-06-08T07:42:25] Annotating alignments 
[2026-06-08T07:43:27] Filtering duplicates (remaining=5894072)
[2026-06-08T07:43:40] 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=3072091)
[2026-06-08T07:43:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3072091)
[2026-06-08T07:43:46] Filtering viral contigs with expression lower than the top 5 (remaining=3072091)
[2026-06-08T07:43:52] Filtering viral contigs with less than 5% coverage (remaining=3072091)
[2026-06-08T07:43:55] Estimating fragment length (mate gap mean=-49.2513, mate gap stddev=26.9705, read length mean=77.4842)
[2026-06-08T07:43:56] Filtering read-through fragments with a distance <=10000bp (remaining=3027523)
[2026-06-08T07:43:58] Filtering inconsistently clipped mates (remaining=3000059)
[2026-06-08T07:44:01] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2883286)
[2026-06-08T07:44:06] Filtering fragments with small insert size (remaining=2882277)
[2026-06-08T07:44:08] Filtering alignments with long gaps (remaining=2882277)
[2026-06-08T07:44:11] Filtering fragments with both mates in the same gene (remaining=2881086)
[2026-06-08T07:44:14] Filtering fusions arising from hairpin structures (remaining=2841922)
[2026-06-08T07:44:17] Filtering reads with a mismatch p-value <=0.01 (remaining=661295)
[2026-06-08T07:44:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=350673)
[2026-06-08T07:44:33] Finding fusions and counting supporting reads (total=343269)
[2026-06-08T07:44:57] Merging adjacent fusion breakpoints (remaining=341512)
[2026-06-08T07:44:59] Filtering multi-mapping fusions by alignment score and read support (remaining=95746)
[2026-06-08T07:45:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:45:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=92564)
[2026-06-08T07:45:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=89735)
[2026-06-08T07:45:55] Filtering fusions with <2 supporting reads (remaining=2416)
[2026-06-08T07:45:56] Filtering fusions with an e-value >=0.3 (remaining=483)
[2026-06-08T07:45:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=489)
[2026-06-08T07:46:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=461)
[2026-06-08T07:46:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=461)
[2026-06-08T07:46:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=452)
[2026-06-08T07:46:13] Searching for fusions with spliced split reads (remaining=464)
[2026-06-08T07:46:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=381)
[2026-06-08T07:46:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=380)
[2026-06-08T07:46:24] Searching for fusions with >=4 spliced events (remaining=383)
[2026-06-08T07:46:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=159)
[2026-06-08T07:46:44] Filtering fusions with anchors <=23nt (remaining=78)
[2026-06-08T07:46:45] Filtering end-to-end fusions with low support (remaining=74)
[2026-06-08T07:46:46] Filtering fusions with no coverage around the breakpoints (remaining=71)
[2026-06-08T07:46:47] Indexing gene sequences 
[2026-06-08T07:46:50] Filtering genes with >=30% identity (remaining=53)
[2026-06-08T07:46:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=44)
[2026-06-08T07:46:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=44)
[2026-06-08T07:46:54] Searching for additional isoforms (remaining=48)
[2026-06-08T07:46:56] Assigning confidence scores to events 
[2026-06-08T07:47:01] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:47:01] Writing fusions to file '1173_LAF_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:47:02] Writing discarded fusions to file '1173_LAF_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:47:37] Freeing resources
[2026-06-08T07:48:08] Done (elapsed time=00:10:11, CPU time=00:10:10, peak memory=19gb)