[2026-06-08T08:41:29] Launching Arriba 2.4.0
[2026-06-08T08:41:29] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:41:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:41:44] Reading chimeric alignments from '1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=15587611)
[2026-06-08T08:48:25] Marking multi-mapping alignments (marked=11429440)
[2026-06-08T08:48:30] Detecting strandedness (reverse)
[2026-06-08T08:48:30] Assigning strands to alignments 
[2026-06-08T08:48:33] Annotating alignments 
[2026-06-08T08:49:14] Filtering duplicates (remaining=7748646)
[2026-06-08T08:49:23] 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=6777836)
[2026-06-08T08:49:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6777836)
[2026-06-08T08:49:29] Filtering viral contigs with expression lower than the top 5 (remaining=6777836)
[2026-06-08T08:49:35] Filtering viral contigs with less than 5% coverage (remaining=6777836)
[2026-06-08T08:49:38] Estimating fragment length (mate gap mean=-77.3486, mate gap stddev=27.0856, read length mean=114.476)
[2026-06-08T08:49:38] Filtering read-through fragments with a distance <=10000bp (remaining=6559106)
[2026-06-08T08:49:41] Filtering inconsistently clipped mates (remaining=6451091)
[2026-06-08T08:49:44] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6312102)
[2026-06-08T08:49:49] Filtering fragments with small insert size (remaining=6310612)
[2026-06-08T08:49:52] Filtering alignments with long gaps (remaining=6310611)
[2026-06-08T08:49:55] Filtering fragments with both mates in the same gene (remaining=6309256)
[2026-06-08T08:49:58] Filtering fusions arising from hairpin structures (remaining=6049799)
[2026-06-08T08:50:01] Filtering reads with a mismatch p-value <=0.01 (remaining=2569327)
[2026-06-08T08:50:14] Filtering reads with low entropy (k-mer content >=60%) (remaining=974477)
[2026-06-08T08:50:25] Finding fusions and counting supporting reads (total=855126)
[2026-06-08T08:50:45] Merging adjacent fusion breakpoints (remaining=846935)
[2026-06-08T08:50:47] Filtering multi-mapping fusions by alignment score and read support (remaining=405524)
[2026-06-08T08:51:26] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:51:34] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=404527)
[2026-06-08T08:51:35] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=310257)
[2026-06-08T08:51:36] Filtering fusions with <2 supporting reads (remaining=15795)
[2026-06-08T08:51:37] Filtering fusions with an e-value >=0.3 (remaining=3211)
[2026-06-08T08:51:37] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3274)
[2026-06-08T08:51:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3192)
[2026-06-08T08:51:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3192)
[2026-06-08T08:51:45] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3177)
[2026-06-08T08:51:51] Searching for fusions with spliced split reads (remaining=3238)
[2026-06-08T08:51:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=2406)
[2026-06-08T08:51:59] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2376)
[2026-06-08T08:52:00] Searching for fusions with >=4 spliced events (remaining=2666)
[2026-06-08T08:52:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1037)
[2026-06-08T08:52:14] Filtering fusions with anchors <=23nt (remaining=833)
[2026-06-08T08:52:15] Filtering end-to-end fusions with low support (remaining=809)
[2026-06-08T08:52:15] Filtering fusions with no coverage around the breakpoints (remaining=792)
[2026-06-08T08:52:16] Indexing gene sequences 
[2026-06-08T08:52:20] Filtering genes with >=30% identity (remaining=306)
[2026-06-08T08:52:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=165)
[2026-06-08T08:52:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=155)
[2026-06-08T08:52:26] Searching for additional isoforms (remaining=176)
[2026-06-08T08:52:28] Assigning confidence scores to events 
[2026-06-08T08:52:32] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:52:32] Writing fusions to file '1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:52:33] Writing discarded fusions to file '1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:53:03] Freeing resources
[2026-06-08T08:53:25] Done (elapsed time=00:11:56, CPU time=00:11:55, peak memory=19.9gb)