[2026-06-03T20:13:11] Launching Arriba 2.4.0
[2026-06-03T20:13:11] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:13:20] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:13:24] Reading chimeric alignments from 'aih-tih-sc-c400f1-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11116301)
[2026-06-03T20:20:26] Marking multi-mapping alignments (marked=7717869)
[2026-06-03T20:20:31] Detecting strandedness (reverse)
[2026-06-03T20:20:31] Assigning strands to alignments 
[2026-06-03T20:20:34] Annotating alignments 
[2026-06-03T20:21:15] Filtering duplicates (remaining=6645029)
[2026-06-03T20:21:24] 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=6101929)
[2026-06-03T20:21:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6101929)
[2026-06-03T20:21:29] Filtering viral contigs with expression lower than the top 5 (remaining=6101929)
[2026-06-03T20:21:34] Filtering viral contigs with less than 5% coverage (remaining=6101929)
[2026-06-03T20:21:37] Estimating fragment length (mate gap mean=-83.959, mate gap stddev=29.2576, read length mean=123.836)
[2026-06-03T20:21:37] Filtering read-through fragments with a distance <=10000bp (remaining=5740532)
[2026-06-03T20:21:39] Filtering inconsistently clipped mates (remaining=5613547)
[2026-06-03T20:21:42] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5443563)
[2026-06-03T20:21:47] Filtering fragments with small insert size (remaining=5442221)
[2026-06-03T20:21:50] Filtering alignments with long gaps (remaining=5442221)
[2026-06-03T20:21:52] Filtering fragments with both mates in the same gene (remaining=5441085)
[2026-06-03T20:21:55] Filtering fusions arising from hairpin structures (remaining=5059063)
[2026-06-03T20:21:58] Filtering reads with a mismatch p-value <=0.01 (remaining=2077284)
[2026-06-03T20:22:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=943765)
[2026-06-03T20:22:24] Finding fusions and counting supporting reads (total=760774)
[2026-06-03T20:22:44] Merging adjacent fusion breakpoints (remaining=752268)
[2026-06-03T20:22:46] Filtering multi-mapping fusions by alignment score and read support (remaining=446330)
[2026-06-03T20:23:26] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:23:33] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=444294)
[2026-06-03T20:23:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=258807)
[2026-06-03T20:23:35] Filtering fusions with <2 supporting reads (remaining=26424)
[2026-06-03T20:23:36] Filtering fusions with an e-value >=0.3 (remaining=6585)
[2026-06-03T20:23:37] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6649)
[2026-06-03T20:23:41] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6554)
[2026-06-03T20:23:42] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6554)
[2026-06-03T20:23:44] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5883)
[2026-06-03T20:23:50] Searching for fusions with spliced split reads (remaining=6011)
[2026-06-03T20:23:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=3848)
[2026-06-03T20:23:57] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3811)
[2026-06-03T20:23:58] Searching for fusions with >=4 spliced events (remaining=4632)
[2026-06-03T20:23:59] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1955)
[2026-06-03T20:24:15] Filtering fusions with anchors <=23nt (remaining=1554)
[2026-06-03T20:24:16] Filtering end-to-end fusions with low support (remaining=1492)
[2026-06-03T20:24:17] Filtering fusions with no coverage around the breakpoints (remaining=1468)
[2026-06-03T20:24:17] Indexing gene sequences 
[2026-06-03T20:24:24] Filtering genes with >=30% identity (remaining=470)
[2026-06-03T20:24:28] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=219)
[2026-06-03T20:24:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=176)
[2026-06-03T20:24:34] Searching for additional isoforms (remaining=221)
[2026-06-03T20:24:35] Assigning confidence scores to events 
[2026-06-03T20:24:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:24:39] Writing fusions to file 'aih-tih-sc-c400f1-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:24:41] Writing discarded fusions to file 'aih-tih-sc-c400f1-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:25:18] Freeing resources
[2026-06-03T20:25:37] Done (elapsed time=00:12:26, CPU time=00:12:24, peak memory=16gb)