[2026-06-03T19:39:34] Launching Arriba 2.4.0
[2026-06-03T19:39:34] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:39:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:39:50] Reading chimeric alignments from 'aih-tih-sc-9703f5-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=7747619)
[2026-06-03T19:45:04] Marking multi-mapping alignments (marked=5548030)
[2026-06-03T19:45:09] Detecting strandedness (reverse)
[2026-06-03T19:45:09] Assigning strands to alignments 
[2026-06-03T19:45:11] Annotating alignments 
[2026-06-03T19:45:55] Filtering duplicates (remaining=3505621)
[2026-06-03T19:46:02] 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=3196108)
[2026-06-03T19:46:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3196108)
[2026-06-03T19:46:07] Filtering viral contigs with expression lower than the top 5 (remaining=3196108)
[2026-06-03T19:46:12] Filtering viral contigs with less than 5% coverage (remaining=3196108)
[2026-06-03T19:46:15] Estimating fragment length (mate gap mean=-80.5457, mate gap stddev=27.2649, read length mean=114.39)
[2026-06-03T19:46:15] Filtering read-through fragments with a distance <=10000bp (remaining=3046275)
[2026-06-03T19:46:18] Filtering inconsistently clipped mates (remaining=2970579)
[2026-06-03T19:46:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2851526)
[2026-06-03T19:46:25] Filtering fragments with small insert size (remaining=2850495)
[2026-06-03T19:46:27] Filtering alignments with long gaps (remaining=2850494)
[2026-06-03T19:46:29] Filtering fragments with both mates in the same gene (remaining=2849617)
[2026-06-03T19:46:32] Filtering fusions arising from hairpin structures (remaining=2675085)
[2026-06-03T19:46:34] Filtering reads with a mismatch p-value <=0.01 (remaining=871696)
[2026-06-03T19:46:42] Filtering reads with low entropy (k-mer content >=60%) (remaining=408481)
[2026-06-03T19:46:50] Finding fusions and counting supporting reads (total=362024)
[2026-06-03T19:47:10] Merging adjacent fusion breakpoints (remaining=358814)
[2026-06-03T19:47:11] Filtering multi-mapping fusions by alignment score and read support (remaining=196821)
[2026-06-03T19:47:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T19:48:03] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=195971)
[2026-06-03T19:48:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=125051)
[2026-06-03T19:48:04] Filtering fusions with <2 supporting reads (remaining=10145)
[2026-06-03T19:48:05] Filtering fusions with an e-value >=0.3 (remaining=2236)
[2026-06-03T19:48:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2284)
[2026-06-03T19:48:09] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2225)
[2026-06-03T19:48:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2225)
[2026-06-03T19:48:12] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2225)
[2026-06-03T19:48:18] Searching for fusions with spliced split reads (remaining=2246)
[2026-06-03T19:48:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=1691)
[2026-06-03T19:48:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1677)
[2026-06-03T19:48:27] Searching for fusions with >=4 spliced events (remaining=1842)
[2026-06-03T19:48:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=687)
[2026-06-03T19:48:49] Filtering fusions with anchors <=23nt (remaining=550)
[2026-06-03T19:48:50] Filtering end-to-end fusions with low support (remaining=528)
[2026-06-03T19:48:50] Filtering fusions with no coverage around the breakpoints (remaining=513)
[2026-06-03T19:48:51] Indexing gene sequences 
[2026-06-03T19:48:55] Filtering genes with >=30% identity (remaining=183)
[2026-06-03T19:48:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=101)
[2026-06-03T19:48:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=83)
[2026-06-03T19:49:00] Searching for additional isoforms (remaining=96)
[2026-06-03T19:49:01] Assigning confidence scores to events 
[2026-06-03T19:49:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T19:49:04] Writing fusions to file 'aih-tih-sc-9703f5-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T19:49:05] Writing discarded fusions to file 'aih-tih-sc-9703f5-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T19:49:38] Freeing resources
[2026-06-03T19:49:58] Done (elapsed time=00:10:24, CPU time=00:10:23, peak memory=12.3gb)