[2026-06-08T08:03:51] Launching Arriba 2.4.0
[2026-06-08T08:03:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:04:08] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:04:13] Reading chimeric alignments from 'aih-tih-sc-64cace-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=2758209)
[2026-06-08T08:06:43] Marking multi-mapping alignments (marked=1678665)
[2026-06-08T08:06:44] Detecting strandedness (reverse)
[2026-06-08T08:06:44] Assigning strands to alignments 
[2026-06-08T08:06:44] Annotating alignments 
[2026-06-08T08:06:54] Filtering duplicates (remaining=2144948)
[2026-06-08T08:06:56] 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=2056327)
[2026-06-08T08:06:57] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2056327)
[2026-06-08T08:06:57] Filtering viral contigs with expression lower than the top 5 (remaining=2056327)
[2026-06-08T08:06:58] Filtering viral contigs with less than 5% coverage (remaining=2056327)
[2026-06-08T08:06:59] Estimating fragment length (mate gap mean=-85.517, mate gap stddev=30.936, read length mean=137.608)
[2026-06-08T08:06:59] Filtering read-through fragments with a distance <=10000bp (remaining=1929619)
[2026-06-08T08:07:00] Filtering inconsistently clipped mates (remaining=1900693)
[2026-06-08T08:07:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1855645)
[2026-06-08T08:07:01] Filtering fragments with small insert size (remaining=1855435)
[2026-06-08T08:07:02] Filtering alignments with long gaps (remaining=1855435)
[2026-06-08T08:07:02] Filtering fragments with both mates in the same gene (remaining=1855067)
[2026-06-08T08:07:03] Filtering fusions arising from hairpin structures (remaining=1747329)
[2026-06-08T08:07:04] Filtering reads with a mismatch p-value <=0.01 (remaining=905978)
[2026-06-08T08:07:08] Filtering reads with low entropy (k-mer content >=60%) (remaining=403496)
[2026-06-08T08:07:12] Finding fusions and counting supporting reads (total=308997)
[2026-06-08T08:07:17] Merging adjacent fusion breakpoints (remaining=307926)
[2026-06-08T08:07:18] Filtering multi-mapping fusions by alignment score and read support (remaining=204459)
[2026-06-08T08:07:27] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:07:29] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=202907)
[2026-06-08T08:07:29] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=114196)
[2026-06-08T08:07:29] Filtering fusions with <2 supporting reads (remaining=17302)
[2026-06-08T08:07:30] Filtering fusions with an e-value >=0.3 (remaining=5814)
[2026-06-08T08:07:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5859)
[2026-06-08T08:07:31] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5842)
[2026-06-08T08:07:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5842)
[2026-06-08T08:07:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4277)
[2026-06-08T08:07:33] Searching for fusions with spliced split reads (remaining=4347)
[2026-06-08T08:07:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=2817)
[2026-06-08T08:07:35] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2775)
[2026-06-08T08:07:35] Searching for fusions with >=4 spliced events (remaining=3016)
[2026-06-08T08:07:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=707)
[2026-06-08T08:07:49] Filtering fusions with anchors <=23nt (remaining=568)
[2026-06-08T08:07:49] Filtering end-to-end fusions with low support (remaining=551)
[2026-06-08T08:07:50] Filtering fusions with no coverage around the breakpoints (remaining=538)
[2026-06-08T08:07:50] Indexing gene sequences 
[2026-06-08T08:07:53] Filtering genes with >=30% identity (remaining=209)
[2026-06-08T08:07:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=139)
[2026-06-08T08:07:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=137)
[2026-06-08T08:07:57] Searching for additional isoforms (remaining=166)
[2026-06-08T08:07:58] Assigning confidence scores to events 
[2026-06-08T08:07:59] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:07:59] Writing fusions to file 'aih-tih-sc-64cace-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:08:00] Writing discarded fusions to file 'aih-tih-sc-64cace-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:08:11] Freeing resources
[2026-06-08T08:08:17] Done (elapsed time=00:04:26, CPU time=00:04:25, peak memory=7.1gb)