[2026-06-03T20:13:12] Launching Arriba 2.4.0
[2026-06-03T20:13:12] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:13:21] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:13:25] Reading chimeric alignments from 'aih-tih-sc-377071-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10493738)
[2026-06-03T20:20:20] Marking multi-mapping alignments (marked=6707265)
[2026-06-03T20:20:25] Detecting strandedness (reverse)
[2026-06-03T20:20:25] Assigning strands to alignments 
[2026-06-03T20:20:27] Annotating alignments 
[2026-06-03T20:21:06] Filtering duplicates (remaining=7243881)
[2026-06-03T20:21:15] 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=6804167)
[2026-06-03T20:21:18] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6804167)
[2026-06-03T20:21:20] Filtering viral contigs with expression lower than the top 5 (remaining=6804167)
[2026-06-03T20:21:25] Filtering viral contigs with less than 5% coverage (remaining=6804167)
[2026-06-03T20:21:28] Estimating fragment length (mate gap mean=-82.7675, mate gap stddev=32.4024, read length mean=133.442)
[2026-06-03T20:21:28] Filtering read-through fragments with a distance <=10000bp (remaining=6430738)
[2026-06-03T20:21:31] Filtering inconsistently clipped mates (remaining=6312086)
[2026-06-03T20:21:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6137055)
[2026-06-03T20:21:39] Filtering fragments with small insert size (remaining=6136195)
[2026-06-03T20:21:41] Filtering alignments with long gaps (remaining=6136194)
[2026-06-03T20:21:44] Filtering fragments with both mates in the same gene (remaining=6134987)
[2026-06-03T20:21:46] Filtering fusions arising from hairpin structures (remaining=5729325)
[2026-06-03T20:21:49] Filtering reads with a mismatch p-value <=0.01 (remaining=2744460)
[2026-06-03T20:22:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=1399754)
[2026-06-03T20:22:19] Finding fusions and counting supporting reads (total=1212611)
[2026-06-03T20:22:39] Merging adjacent fusion breakpoints (remaining=1206763)
[2026-06-03T20:22:42] Filtering multi-mapping fusions by alignment score and read support (remaining=802612)
[2026-06-03T20:23:19] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:23:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=799847)
[2026-06-03T20:23:29] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=592563)
[2026-06-03T20:23:31] Filtering fusions with <2 supporting reads (remaining=40896)
[2026-06-03T20:23:32] Filtering fusions with an e-value >=0.3 (remaining=11646)
[2026-06-03T20:23:32] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11708)
[2026-06-03T20:23:37] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11605)
[2026-06-03T20:23:38] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11605)
[2026-06-03T20:23:40] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7439)
[2026-06-03T20:23:46] Searching for fusions with spliced split reads (remaining=7477)
[2026-06-03T20:23:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=3914)
[2026-06-03T20:23:54] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3857)
[2026-06-03T20:23:55] Searching for fusions with >=4 spliced events (remaining=4678)
[2026-06-03T20:23:57] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1909)
[2026-06-03T20:24:14] Filtering fusions with anchors <=23nt (remaining=1463)
[2026-06-03T20:24:15] Filtering end-to-end fusions with low support (remaining=1425)
[2026-06-03T20:24:15] Filtering fusions with no coverage around the breakpoints (remaining=1390)
[2026-06-03T20:24:16] Indexing gene sequences 
[2026-06-03T20:24:23] Filtering genes with >=30% identity (remaining=432)
[2026-06-03T20:24:26] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=226)
[2026-06-03T20:24:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=212)
[2026-06-03T20:24:35] Searching for additional isoforms (remaining=277)
[2026-06-03T20:24:37] Assigning confidence scores to events 
[2026-06-03T20:24:41] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:24:41] Writing fusions to file 'aih-tih-sc-377071-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:24:45] Writing discarded fusions to file 'aih-tih-sc-377071-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:25:25] Freeing resources
[2026-06-03T20:25:44] Done (elapsed time=00:12:32, CPU time=00:12:31, peak memory=15.4gb)