[2026-06-03T20:38:39] Launching Arriba 2.4.0
[2026-06-03T20:38:39] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:38:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:38:51] Reading chimeric alignments from 'aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11017585)
[2026-06-03T20:45:15] Marking multi-mapping alignments (marked=7224291)
[2026-06-03T20:45:19] Detecting strandedness (reverse)
[2026-06-03T20:45:19] Assigning strands to alignments 
[2026-06-03T20:45:21] Annotating alignments 
[2026-06-03T20:45:53] Filtering duplicates (remaining=6455377)
[2026-06-03T20:46:01] 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=6106867)
[2026-06-03T20:46:03] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6106867)
[2026-06-03T20:46:06] Filtering viral contigs with expression lower than the top 5 (remaining=6106867)
[2026-06-03T20:46:13] Filtering viral contigs with less than 5% coverage (remaining=6106867)
[2026-06-03T20:46:16] Estimating fragment length (mate gap mean=-83.0101, mate gap stddev=28.5078, read length mean=122.361)
[2026-06-03T20:46:16] Filtering read-through fragments with a distance <=10000bp (remaining=5714728)
[2026-06-03T20:46:19] Filtering inconsistently clipped mates (remaining=5584188)
[2026-06-03T20:46:22] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5427153)
[2026-06-03T20:46:28] Filtering fragments with small insert size (remaining=5425884)
[2026-06-03T20:46:31] Filtering alignments with long gaps (remaining=5425884)
[2026-06-03T20:46:34] Filtering fragments with both mates in the same gene (remaining=5424879)
[2026-06-03T20:46:36] Filtering fusions arising from hairpin structures (remaining=5070988)
[2026-06-03T20:46:40] Filtering reads with a mismatch p-value <=0.01 (remaining=2073155)
[2026-06-03T20:46:52] Filtering reads with low entropy (k-mer content >=60%) (remaining=1014955)
[2026-06-03T20:47:03] Finding fusions and counting supporting reads (total=790054)
[2026-06-03T20:47:20] Merging adjacent fusion breakpoints (remaining=779908)
[2026-06-03T20:47:21] Filtering multi-mapping fusions by alignment score and read support (remaining=486465)
[2026-06-03T20:47:55] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:48:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=485035)
[2026-06-03T20:48:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=274053)
[2026-06-03T20:48:04] Filtering fusions with <2 supporting reads (remaining=34038)
[2026-06-03T20:48:05] Filtering fusions with an e-value >=0.3 (remaining=7482)
[2026-06-03T20:48:06] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7540)
[2026-06-03T20:48:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7449)
[2026-06-03T20:48:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7449)
[2026-06-03T20:48:12] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6661)
[2026-06-03T20:48:18] Searching for fusions with spliced split reads (remaining=6764)
[2026-06-03T20:48:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=4458)
[2026-06-03T20:48:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4409)
[2026-06-03T20:48:25] Searching for fusions with >=4 spliced events (remaining=5122)
[2026-06-03T20:48:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2018)
[2026-06-03T20:48:44] Filtering fusions with anchors <=23nt (remaining=1499)
[2026-06-03T20:48:45] Filtering end-to-end fusions with low support (remaining=1452)
[2026-06-03T20:48:45] Filtering fusions with no coverage around the breakpoints (remaining=1426)
[2026-06-03T20:48:46] Indexing gene sequences 
[2026-06-03T20:48:51] Filtering genes with >=30% identity (remaining=396)
[2026-06-03T20:48:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=156)
[2026-06-03T20:48:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=149)
[2026-06-03T20:48:57] Searching for additional isoforms (remaining=188)
[2026-06-03T20:48:59] Assigning confidence scores to events 
[2026-06-03T20:49:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:49:02] Writing fusions to file 'aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:49:04] Writing discarded fusions to file 'aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:49:31] Freeing resources
[2026-06-03T20:49:50] Done (elapsed time=00:11:11, CPU time=00:11:10, peak memory=15.8gb)