[2026-06-08T08:40:34] Launching Arriba 2.4.0
[2026-06-08T08:40:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:40:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:52] Reading chimeric alignments from '1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=14342660)
[2026-06-08T08:49:32] Marking multi-mapping alignments (marked=9696276)
[2026-06-08T08:49:38] Detecting strandedness (reverse)
[2026-06-08T08:49:38] Assigning strands to alignments 
[2026-06-08T08:49:41] Annotating alignments 
[2026-06-08T08:50:29] Filtering duplicates (remaining=10953633)
[2026-06-08T08:50:41] 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=9883909)
[2026-06-08T08:50:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9883909)
[2026-06-08T08:50:47] Filtering viral contigs with expression lower than the top 5 (remaining=9883909)
[2026-06-08T08:50:55] Filtering viral contigs with less than 5% coverage (remaining=9883909)
[2026-06-08T08:50:59] Estimating fragment length (mate gap mean=-81.4854, mate gap stddev=27.7708, read length mean=126.018)
[2026-06-08T08:50:59] Filtering read-through fragments with a distance <=10000bp (remaining=9604299)
[2026-06-08T08:51:02] Filtering inconsistently clipped mates (remaining=9497869)
[2026-06-08T08:51:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9303091)
[2026-06-08T08:51:12] Filtering fragments with small insert size (remaining=9302159)
[2026-06-08T08:51:15] Filtering alignments with long gaps (remaining=9302159)
[2026-06-08T08:51:19] Filtering fragments with both mates in the same gene (remaining=9300216)
[2026-06-08T08:51:22] Filtering fusions arising from hairpin structures (remaining=9044318)
[2026-06-08T08:51:25] Filtering reads with a mismatch p-value <=0.01 (remaining=4585331)
[2026-06-08T08:51:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=2228623)
[2026-06-08T08:52:11] Finding fusions and counting supporting reads (total=2067348)
[2026-06-08T08:52:39] Merging adjacent fusion breakpoints (remaining=2060209)
[2026-06-08T08:52:43] Filtering multi-mapping fusions by alignment score and read support (remaining=1119162)
[2026-06-08T08:53:31] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:53:45] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1117563)
[2026-06-08T08:53:46] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=988654)
[2026-06-08T08:53:48] Filtering fusions with <2 supporting reads (remaining=26747)
[2026-06-08T08:53:49] Filtering fusions with an e-value >=0.3 (remaining=4682)
[2026-06-08T08:53:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4729)
[2026-06-08T08:53:57] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4664)
[2026-06-08T08:53:58] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4664)
[2026-06-08T08:54:01] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4350)
[2026-06-08T08:54:10] Searching for fusions with spliced split reads (remaining=4489)
[2026-06-08T08:54:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=3120)
[2026-06-08T08:54:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3064)
[2026-06-08T08:54:23] Searching for fusions with >=4 spliced events (remaining=3609)
[2026-06-08T08:54:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1312)
[2026-06-08T08:54:42] Filtering fusions with anchors <=23nt (remaining=1068)
[2026-06-08T08:54:43] Filtering end-to-end fusions with low support (remaining=1048)
[2026-06-08T08:54:45] Filtering fusions with no coverage around the breakpoints (remaining=1031)
[2026-06-08T08:54:46] Indexing gene sequences 
[2026-06-08T08:54:52] Filtering genes with >=30% identity (remaining=373)
[2026-06-08T08:54:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=204)
[2026-06-08T08:55:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=173)
[2026-06-08T08:55:04] Searching for additional isoforms (remaining=223)
[2026-06-08T08:55:06] Assigning confidence scores to events 
[2026-06-08T08:55:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:55:12] Writing fusions to file '1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:55:15] Writing discarded fusions to file '1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:56:12] Freeing resources
[2026-06-08T08:56:38] Done (elapsed time=00:16:04, CPU time=00:16:02, peak memory=19.2gb)