[2026-06-08T08:42:33] Launching Arriba 2.4.0
[2026-06-08T08:42:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:42:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:42:53] Reading chimeric alignments from '1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=14591507)
[2026-06-08T08:53:27] Marking multi-mapping alignments (marked=9550114)
[2026-06-08T08:53:35] Detecting strandedness (reverse)
[2026-06-08T08:53:35] Assigning strands to alignments 
[2026-06-08T08:53:38] Annotating alignments 
[2026-06-08T08:54:45] Filtering duplicates (remaining=10494367)
[2026-06-08T08:55:00] 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=9888143)
[2026-06-08T08:55:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9888143)
[2026-06-08T08:55:08] Filtering viral contigs with expression lower than the top 5 (remaining=9888143)
[2026-06-08T08:55:16] Filtering viral contigs with less than 5% coverage (remaining=9888143)
[2026-06-08T08:55:20] Estimating fragment length (mate gap mean=-85.5793, mate gap stddev=27.951, read length mean=131.298)
[2026-06-08T08:55:20] Filtering read-through fragments with a distance <=10000bp (remaining=9538616)
[2026-06-08T08:55:24] Filtering inconsistently clipped mates (remaining=9389902)
[2026-06-08T08:55:27] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9188570)
[2026-06-08T08:55:35] Filtering fragments with small insert size (remaining=9187437)
[2026-06-08T08:55:39] Filtering alignments with long gaps (remaining=9187437)
[2026-06-08T08:55:43] Filtering fragments with both mates in the same gene (remaining=9185949)
[2026-06-08T08:55:48] Filtering fusions arising from hairpin structures (remaining=8785458)
[2026-06-08T08:55:53] Filtering reads with a mismatch p-value <=0.01 (remaining=4389999)
[2026-06-08T08:56:25] Filtering reads with low entropy (k-mer content >=60%) (remaining=1983081)
[2026-06-08T08:56:49] Finding fusions and counting supporting reads (total=1757865)
[2026-06-08T08:57:27] Merging adjacent fusion breakpoints (remaining=1749551)
[2026-06-08T08:57:32] Filtering multi-mapping fusions by alignment score and read support (remaining=1006606)
[2026-06-08T08:58:58] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:19] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1004627)
[2026-06-08T08:59:21] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=824558)
[2026-06-08T08:59:23] Filtering fusions with <2 supporting reads (remaining=30648)
[2026-06-08T08:59:25] Filtering fusions with an e-value >=0.3 (remaining=5805)
[2026-06-08T08:59:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5875)
[2026-06-08T08:59:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5807)
[2026-06-08T08:59:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5807)
[2026-06-08T08:59:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5235)
[2026-06-08T08:59:55] Searching for fusions with spliced split reads (remaining=5387)
[2026-06-08T09:00:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=3636)
[2026-06-08T09:00:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3574)
[2026-06-08T09:00:15] Searching for fusions with >=4 spliced events (remaining=4301)
[2026-06-08T09:00:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1641)
[2026-06-08T09:00:42] Filtering fusions with anchors <=23nt (remaining=1356)
[2026-06-08T09:00:44] Filtering end-to-end fusions with low support (remaining=1320)
[2026-06-08T09:00:46] Filtering fusions with no coverage around the breakpoints (remaining=1285)
[2026-06-08T09:00:48] Indexing gene sequences 
[2026-06-08T09:01:04] Filtering genes with >=30% identity (remaining=406)
[2026-06-08T09:01:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=207)
[2026-06-08T09:01:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=188)
[2026-06-08T09:01:24] Searching for additional isoforms (remaining=231)
[2026-06-08T09:01:28] Assigning confidence scores to events 
[2026-06-08T09:01:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:39] Writing fusions to file '1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T09:01:43] Writing discarded fusions to file '1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:03:17] Freeing resources
[2026-06-08T09:03:53] Done (elapsed time=00:21:20, CPU time=00:21:19, peak memory=19.3gb)