[2026-06-08T07:33:53] Launching Arriba 2.4.0
[2026-06-08T07:33:53] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:34:11] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:34:16] Reading chimeric alignments from '1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=1707211)
[2026-06-08T07:35:32] Marking multi-mapping alignments (marked=1188972)
[2026-06-08T07:35:33] Detecting strandedness (reverse)
[2026-06-08T07:35:33] Assigning strands to alignments 
[2026-06-08T07:35:33] Annotating alignments 
[2026-06-08T07:35:39] Filtering duplicates (remaining=1327156)
[2026-06-08T07:35:41] 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=1192277)
[2026-06-08T07:35:41] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1192277)
[2026-06-08T07:35:42] Filtering viral contigs with expression lower than the top 5 (remaining=1192277)
[2026-06-08T07:35:42] Filtering viral contigs with less than 5% coverage (remaining=1192277)
[2026-06-08T07:35:43] Estimating fragment length (mate gap mean=-78.7287, mate gap stddev=26.3286, read length mean=116.698)
[2026-06-08T07:35:43] Filtering read-through fragments with a distance <=10000bp (remaining=1156578)
[2026-06-08T07:35:43] Filtering inconsistently clipped mates (remaining=1123364)
[2026-06-08T07:35:44] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1099196)
[2026-06-08T07:35:44] Filtering fragments with small insert size (remaining=1098960)
[2026-06-08T07:35:45] Filtering alignments with long gaps (remaining=1098960)
[2026-06-08T07:35:45] Filtering fragments with both mates in the same gene (remaining=1098763)
[2026-06-08T07:35:46] Filtering fusions arising from hairpin structures (remaining=1014437)
[2026-06-08T07:35:46] Filtering reads with a mismatch p-value <=0.01 (remaining=518429)
[2026-06-08T07:35:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=238259)
[2026-06-08T07:35:52] Finding fusions and counting supporting reads (total=220931)
[2026-06-08T07:35:56] Merging adjacent fusion breakpoints (remaining=219853)
[2026-06-08T07:35:56] Filtering multi-mapping fusions by alignment score and read support (remaining=115266)
[2026-06-08T07:36:03] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:36:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=114922)
[2026-06-08T07:36:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=88436)
[2026-06-08T07:36:05] Filtering fusions with <2 supporting reads (remaining=3249)
[2026-06-08T07:36:05] Filtering fusions with an e-value >=0.3 (remaining=916)
[2026-06-08T07:36:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1009)
[2026-06-08T07:36:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=994)
[2026-06-08T07:36:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=994)
[2026-06-08T07:36:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=990)
[2026-06-08T07:36:08] Searching for fusions with spliced split reads (remaining=1038)
[2026-06-08T07:36:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=829)
[2026-06-08T07:36:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=821)
[2026-06-08T07:36:10] Searching for fusions with >=4 spliced events (remaining=854)
[2026-06-08T07:36:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=242)
[2026-06-08T07:36:28] Filtering fusions with anchors <=23nt (remaining=215)
[2026-06-08T07:36:29] Filtering end-to-end fusions with low support (remaining=206)
[2026-06-08T07:36:29] Filtering fusions with no coverage around the breakpoints (remaining=198)
[2026-06-08T07:36:29] Indexing gene sequences 
[2026-06-08T07:36:31] Filtering genes with >=30% identity (remaining=103)
[2026-06-08T07:36:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=81)
[2026-06-08T07:36:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=77)
[2026-06-08T07:36:34] Searching for additional isoforms (remaining=86)
[2026-06-08T07:36:34] Assigning confidence scores to events 
[2026-06-08T07:36:35] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:36:35] Writing fusions to file '1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:36:36] Writing discarded fusions to file '1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:36:46] Freeing resources
[2026-06-08T07:36:50] Done (elapsed time=00:02:57, CPU time=00:02:57, peak memory=5.92gb)