[2026-06-08T07:51:02] Launching Arriba 2.4.0
[2026-06-08T07:51:02] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:51:20] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:51:25] Reading chimeric alignments from '1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=4784443)
[2026-06-08T07:55:24] Marking multi-mapping alignments (marked=3280397)
[2026-06-08T07:55:27] Detecting strandedness (reverse)
[2026-06-08T07:55:27] Assigning strands to alignments 
[2026-06-08T07:55:27] Annotating alignments 
[2026-06-08T07:55:46] Filtering duplicates (remaining=3965407)
[2026-06-08T07:55:50] 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=3513343)
[2026-06-08T07:55:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3513343)
[2026-06-08T07:55:52] Filtering viral contigs with expression lower than the top 5 (remaining=3513343)
[2026-06-08T07:55:55] Filtering viral contigs with less than 5% coverage (remaining=3513343)
[2026-06-08T07:55:56] Estimating fragment length (mate gap mean=-82.774, mate gap stddev=26.952, read length mean=123.046)
[2026-06-08T07:55:56] Filtering read-through fragments with a distance <=10000bp (remaining=3378970)
[2026-06-08T07:55:57] Filtering inconsistently clipped mates (remaining=3342118)
[2026-06-08T07:55:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3281024)
[2026-06-08T07:56:01] Filtering fragments with small insert size (remaining=3280691)
[2026-06-08T07:56:02] Filtering alignments with long gaps (remaining=3280691)
[2026-06-08T07:56:03] Filtering fragments with both mates in the same gene (remaining=3280052)
[2026-06-08T07:56:05] Filtering fusions arising from hairpin structures (remaining=3193000)
[2026-06-08T07:56:06] Filtering reads with a mismatch p-value <=0.01 (remaining=1624420)
[2026-06-08T07:56:16] Filtering reads with low entropy (k-mer content >=60%) (remaining=797354)
[2026-06-08T07:56:24] Finding fusions and counting supporting reads (total=765845)
[2026-06-08T07:56:36] Merging adjacent fusion breakpoints (remaining=763441)
[2026-06-08T07:56:37] Filtering multi-mapping fusions by alignment score and read support (remaining=411958)
[2026-06-08T07:56:56] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:57:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=411472)
[2026-06-08T07:57:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=358649)
[2026-06-08T07:57:02] Filtering fusions with <2 supporting reads (remaining=9877)
[2026-06-08T07:57:03] Filtering fusions with an e-value >=0.3 (remaining=1910)
[2026-06-08T07:57:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1961)
[2026-06-08T07:57:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1938)
[2026-06-08T07:57:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1938)
[2026-06-08T07:57:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1933)
[2026-06-08T07:57:11] Searching for fusions with spliced split reads (remaining=2076)
[2026-06-08T07:57:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=1562)
[2026-06-08T07:57:15] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1550)
[2026-06-08T07:57:16] Searching for fusions with >=4 spliced events (remaining=1705)
[2026-06-08T07:57:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=699)
[2026-06-08T07:57:32] Filtering fusions with anchors <=23nt (remaining=553)
[2026-06-08T07:57:33] Filtering end-to-end fusions with low support (remaining=543)
[2026-06-08T07:57:33] Filtering fusions with no coverage around the breakpoints (remaining=531)
[2026-06-08T07:57:34] Indexing gene sequences 
[2026-06-08T07:57:37] Filtering genes with >=30% identity (remaining=215)
[2026-06-08T07:57:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=129)
[2026-06-08T07:57:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=129)
[2026-06-08T07:57:40] Searching for additional isoforms (remaining=142)
[2026-06-08T07:57:41] Assigning confidence scores to events 
[2026-06-08T07:57:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:57:44] Writing fusions to file '1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:57:45] Writing discarded fusions to file '1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:58:14] Freeing resources
[2026-06-08T07:58:25] Done (elapsed time=00:07:23, CPU time=00:07:22, peak memory=9.27gb)