[2026-06-08T08:41:33] Launching Arriba 2.4.0
[2026-06-08T08:41:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:41:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:41:51] Reading chimeric alignments from '1173_JLC_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=14707765)
[2026-06-08T08:49:34] Marking multi-mapping alignments (marked=9682155)
[2026-06-08T08:49:40] Detecting strandedness (reverse)
[2026-06-08T08:49:40] Assigning strands to alignments 
[2026-06-08T08:49:43] Annotating alignments 
[2026-06-08T08:50:27] Filtering duplicates (remaining=11456318)
[2026-06-08T08:50:38] 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=10173462)
[2026-06-08T08:50:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=10173462)
[2026-06-08T08:50:43] Filtering viral contigs with expression lower than the top 5 (remaining=10173462)
[2026-06-08T08:50:50] Filtering viral contigs with less than 5% coverage (remaining=10173462)
[2026-06-08T08:50:53] Estimating fragment length (mate gap mean=-82.8784, mate gap stddev=28.3475, read length mean=129.342)
[2026-06-08T08:50:53] Filtering read-through fragments with a distance <=10000bp (remaining=9853842)
[2026-06-08T08:50:56] Filtering inconsistently clipped mates (remaining=9752331)
[2026-06-08T08:50:59] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9570153)
[2026-06-08T08:51:06] Filtering fragments with small insert size (remaining=9569258)
[2026-06-08T08:51:09] Filtering alignments with long gaps (remaining=9569256)
[2026-06-08T08:51:11] Filtering fragments with both mates in the same gene (remaining=9567796)
[2026-06-08T08:51:14] Filtering fusions arising from hairpin structures (remaining=9300697)
[2026-06-08T08:51:18] Filtering reads with a mismatch p-value <=0.01 (remaining=5165311)
[2026-06-08T08:51:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=2865797)
[2026-06-08T08:51:58] Finding fusions and counting supporting reads (total=2777239)
[2026-06-08T08:52:24] Merging adjacent fusion breakpoints (remaining=2769593)
[2026-06-08T08:52:28] Filtering multi-mapping fusions by alignment score and read support (remaining=1531000)
[2026-06-08T08:53:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:53:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1529314)
[2026-06-08T08:53:26] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1377518)
[2026-06-08T08:53:27] Filtering fusions with <2 supporting reads (remaining=40721)
[2026-06-08T08:53:28] Filtering fusions with an e-value >=0.3 (remaining=6538)
[2026-06-08T08:53:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6609)
[2026-06-08T08:53:35] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6542)
[2026-06-08T08:53:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6542)
[2026-06-08T08:53:40] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5067)
[2026-06-08T08:53:48] Searching for fusions with spliced split reads (remaining=5197)
[2026-06-08T08:53:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=3535)
[2026-06-08T08:53:59] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3471)
[2026-06-08T08:54:00] Searching for fusions with >=4 spliced events (remaining=4221)
[2026-06-08T08:54:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1556)
[2026-06-08T08:54:18] Filtering fusions with anchors <=23nt (remaining=1192)
[2026-06-08T08:54:19] Filtering end-to-end fusions with low support (remaining=1165)
[2026-06-08T08:54:20] Filtering fusions with no coverage around the breakpoints (remaining=1152)
[2026-06-08T08:54:22] Indexing gene sequences 
[2026-06-08T08:54:28] Filtering genes with >=30% identity (remaining=425)
[2026-06-08T08:54:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=261)
[2026-06-08T08:54:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=207)
[2026-06-08T08:54:39] Searching for additional isoforms (remaining=265)
[2026-06-08T08:54:41] Assigning confidence scores to events 
[2026-06-08T08:54:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:54:48] Writing fusions to file '1173_JLC_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:54:50] Writing discarded fusions to file '1173_JLC_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:55:41] Freeing resources
[2026-06-08T08:56:04] Done (elapsed time=00:14:31, CPU time=00:14:30, peak memory=20gb)