[2026-06-03T20:35:41] Launching Arriba 2.4.0
[2026-06-03T20:35:41] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:35:49] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:35:53] Reading chimeric alignments from 'aih-tih-sc-966ec5-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=12366896)
[2026-06-03T20:42:29] Marking multi-mapping alignments (marked=8508056)
[2026-06-03T20:42:34] Detecting strandedness (reverse)
[2026-06-03T20:42:34] Assigning strands to alignments 
[2026-06-03T20:42:36] Annotating alignments 
[2026-06-03T20:43:16] Filtering duplicates (remaining=7321672)
[2026-06-03T20:43:23] 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=6757999)
[2026-06-03T20:43:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6757999)
[2026-06-03T20:43:28] Filtering viral contigs with expression lower than the top 5 (remaining=6757999)
[2026-06-03T20:43:34] Filtering viral contigs with less than 5% coverage (remaining=6757999)
[2026-06-03T20:43:36] Estimating fragment length (mate gap mean=-83.7711, mate gap stddev=28.8585, read length mean=122.057)
[2026-06-03T20:43:36] Filtering read-through fragments with a distance <=10000bp (remaining=6413409)
[2026-06-03T20:43:39] Filtering inconsistently clipped mates (remaining=6264042)
[2026-06-03T20:43:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6094749)
[2026-06-03T20:43:46] Filtering fragments with small insert size (remaining=6093293)
[2026-06-03T20:43:49] Filtering alignments with long gaps (remaining=6093293)
[2026-06-03T20:43:51] Filtering fragments with both mates in the same gene (remaining=6092066)
[2026-06-03T20:43:54] Filtering fusions arising from hairpin structures (remaining=5679500)
[2026-06-03T20:43:57] Filtering reads with a mismatch p-value <=0.01 (remaining=2268339)
[2026-06-03T20:44:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=1095980)
[2026-06-03T20:44:21] Finding fusions and counting supporting reads (total=926667)
[2026-06-03T20:44:40] Merging adjacent fusion breakpoints (remaining=913959)
[2026-06-03T20:44:42] Filtering multi-mapping fusions by alignment score and read support (remaining=554482)
[2026-06-03T20:45:19] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:45:27] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=552850)
[2026-06-03T20:45:28] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=378110)
[2026-06-03T20:45:29] Filtering fusions with <2 supporting reads (remaining=29527)
[2026-06-03T20:45:30] Filtering fusions with an e-value >=0.3 (remaining=5844)
[2026-06-03T20:45:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5906)
[2026-06-03T20:45:35] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5749)
[2026-06-03T20:45:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5751)
[2026-06-03T20:45:38] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5647)
[2026-06-03T20:45:44] Searching for fusions with spliced split reads (remaining=5762)
[2026-06-03T20:45:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=4012)
[2026-06-03T20:45:52] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3982)
[2026-06-03T20:45:53] Searching for fusions with >=4 spliced events (remaining=4766)
[2026-06-03T20:45:55] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2004)
[2026-06-03T20:46:13] Filtering fusions with anchors <=23nt (remaining=1514)
[2026-06-03T20:46:14] Filtering end-to-end fusions with low support (remaining=1475)
[2026-06-03T20:46:14] Filtering fusions with no coverage around the breakpoints (remaining=1450)
[2026-06-03T20:46:15] Indexing gene sequences 
[2026-06-03T20:46:22] Filtering genes with >=30% identity (remaining=439)
[2026-06-03T20:46:24] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=186)
[2026-06-03T20:46:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=162)
[2026-06-03T20:46:28] Searching for additional isoforms (remaining=213)
[2026-06-03T20:46:30] Assigning confidence scores to events 
[2026-06-03T20:46:34] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:46:34] Writing fusions to file 'aih-tih-sc-966ec5-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:46:36] Writing discarded fusions to file 'aih-tih-sc-966ec5-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:47:08] Freeing resources
[2026-06-03T20:47:27] Done (elapsed time=00:11:46, CPU time=00:11:45, peak memory=17.3gb)