[2026-06-08T08:38:36] Launching Arriba 2.4.0
[2026-06-08T08:38:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:38:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:38:51] Reading chimeric alignments from '1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=15903680)
[2026-06-08T08:47:35] Marking multi-mapping alignments (marked=11515997)
[2026-06-08T08:47:43] Detecting strandedness (no)
[2026-06-08T08:47:43] Annotating alignments 
[2026-06-08T08:49:14] Filtering duplicates (remaining=11596155)
[2026-06-08T08:49:41] 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=10006635)
[2026-06-08T08:49:46] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=10006635)
[2026-06-08T08:49:50] Filtering viral contigs with expression lower than the top 5 (remaining=10006635)
[2026-06-08T08:50:02] Filtering viral contigs with less than 5% coverage (remaining=10006635)
[2026-06-08T08:50:07] Estimating fragment length (mate gap mean=-78.7366, mate gap stddev=27.195, read length mean=119.581)
[2026-06-08T08:50:07] Filtering read-through fragments with a distance <=10000bp (remaining=9593355)
[2026-06-08T08:50:12] Filtering inconsistently clipped mates (remaining=9475545)
[2026-06-08T08:50:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9296953)
[2026-06-08T08:50:28] Filtering fragments with small insert size (remaining=9295743)
[2026-06-08T08:50:32] Filtering alignments with long gaps (remaining=9295743)
[2026-06-08T08:50:38] Filtering fragments with both mates in the same gene (remaining=9293910)
[2026-06-08T08:50:44] Filtering fusions arising from hairpin structures (remaining=8977918)
[2026-06-08T08:50:49] Filtering reads with a mismatch p-value <=0.01 (remaining=4407451)
[2026-06-08T08:51:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=2294536)
[2026-06-08T08:51:47] Finding fusions and counting supporting reads (total=2132164)
[2026-06-08T08:52:34] Merging adjacent fusion breakpoints (remaining=2119474)
[2026-06-08T08:52:40] Filtering multi-mapping fusions by alignment score and read support (remaining=1034006)
[2026-06-08T08:54:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:54:45] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1032834)
[2026-06-08T08:54:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=898082)
[2026-06-08T08:54:51] Filtering fusions with <2 supporting reads (remaining=22647)
[2026-06-08T08:54:54] Filtering fusions with an e-value >=0.3 (remaining=3659)
[2026-06-08T08:54:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3721)
[2026-06-08T08:55:07] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3654)
[2026-06-08T08:55:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3654)
[2026-06-08T08:55:16] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3615)
[2026-06-08T08:55:34] Searching for fusions with spliced split reads (remaining=3714)
[2026-06-08T08:55:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=2685)
[2026-06-08T08:55:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2653)
[2026-06-08T08:56:01] Searching for fusions with >=4 spliced events (remaining=3140)
[2026-06-08T08:56:06] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1386)
[2026-06-08T08:56:34] Filtering fusions with anchors <=23nt (remaining=1038)
[2026-06-08T08:56:37] Filtering end-to-end fusions with low support (remaining=1015)
[2026-06-08T08:56:39] Filtering fusions with no coverage around the breakpoints (remaining=1005)
[2026-06-08T08:56:42] Indexing gene sequences 
[2026-06-08T08:56:53] Filtering genes with >=30% identity (remaining=342)
[2026-06-08T08:56:58] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=179)
[2026-06-08T08:57:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=151)
[2026-06-08T08:57:10] Searching for additional isoforms (remaining=185)
[2026-06-08T08:57:15] Assigning confidence scores to events 
[2026-06-08T08:57:28] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:57:28] Writing fusions to file '1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:57:32] Writing discarded fusions to file '1173_DSO_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:17] Freeing resources
[2026-06-08T09:00:13] Done (elapsed time=00:21:37, CPU time=00:21:36, peak memory=21gb)