[2026-06-03T20:17:48] Launching Arriba 2.4.0
[2026-06-03T20:17:48] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:17:56] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:17:59] Reading chimeric alignments from 'aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9571678)
[2026-06-03T20:24:57] Marking multi-mapping alignments (marked=5980750)
[2026-06-03T20:25:01] Detecting strandedness (reverse)
[2026-06-03T20:25:01] Assigning strands to alignments 
[2026-06-03T20:25:03] Annotating alignments 
[2026-06-03T20:25:35] Filtering duplicates (remaining=7159062)
[2026-06-03T20:25:42] 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=6793309)
[2026-06-03T20:25:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6793309)
[2026-06-03T20:25:46] Filtering viral contigs with expression lower than the top 5 (remaining=6793309)
[2026-06-03T20:25:51] Filtering viral contigs with less than 5% coverage (remaining=6793309)
[2026-06-03T20:25:53] Estimating fragment length (mate gap mean=-85.1878, mate gap stddev=31.7573, read length mean=137.201)
[2026-06-03T20:25:53] Filtering read-through fragments with a distance <=10000bp (remaining=6449944)
[2026-06-03T20:25:55] Filtering inconsistently clipped mates (remaining=6349920)
[2026-06-03T20:25:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6164143)
[2026-06-03T20:26:02] Filtering fragments with small insert size (remaining=6163631)
[2026-06-03T20:26:04] Filtering alignments with long gaps (remaining=6163630)
[2026-06-03T20:26:06] Filtering fragments with both mates in the same gene (remaining=6162280)
[2026-06-03T20:26:08] Filtering fusions arising from hairpin structures (remaining=5758823)
[2026-06-03T20:26:11] Filtering reads with a mismatch p-value <=0.01 (remaining=2800962)
[2026-06-03T20:26:25] Filtering reads with low entropy (k-mer content >=60%) (remaining=1357668)
[2026-06-03T20:26:37] Finding fusions and counting supporting reads (total=1058894)
[2026-06-03T20:26:55] Merging adjacent fusion breakpoints (remaining=1051242)
[2026-06-03T20:26:57] Filtering multi-mapping fusions by alignment score and read support (remaining=703557)
[2026-06-03T20:27:28] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:27:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=700045)
[2026-06-03T20:27:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=457908)
[2026-06-03T20:27:38] Filtering fusions with <2 supporting reads (remaining=60035)
[2026-06-03T20:27:39] Filtering fusions with an e-value >=0.3 (remaining=30211)
[2026-06-03T20:27:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=30265)
[2026-06-03T20:27:43] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=30179)
[2026-06-03T20:27:44] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=30179)
[2026-06-03T20:27:46] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9131)
[2026-06-03T20:27:51] Searching for fusions with spliced split reads (remaining=9183)
[2026-06-03T20:27:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=4346)
[2026-06-03T20:27:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4306)
[2026-06-03T20:27:59] Searching for fusions with >=4 spliced events (remaining=5713)
[2026-06-03T20:28:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2533)
[2026-06-03T20:28:15] Filtering fusions with anchors <=23nt (remaining=2076)
[2026-06-03T20:28:16] Filtering end-to-end fusions with low support (remaining=2014)
[2026-06-03T20:28:16] Filtering fusions with no coverage around the breakpoints (remaining=1973)
[2026-06-03T20:28:17] Indexing gene sequences 
[2026-06-03T20:28:24] Filtering genes with >=30% identity (remaining=679)
[2026-06-03T20:28:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=409)
[2026-06-03T20:28:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=259)
[2026-06-03T20:28:35] Searching for additional isoforms (remaining=450)
[2026-06-03T20:28:36] Assigning confidence scores to events 
[2026-06-03T20:28:40] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:28:40] Writing fusions to file 'aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:28:44] Writing discarded fusions to file 'aih-tih-sc-6c4b48-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:29:15] Freeing resources
[2026-06-03T20:29:32] Done (elapsed time=00:11:44, CPU time=00:11:43, peak memory=14.5gb)