[2026-06-03T21:02:44] Launching Arriba 2.4.0
[2026-06-03T21:02:44] Loading assembly from 'ref_genome.fa' 
[2026-06-03T21:02:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T21:02:57] Reading chimeric alignments from 'aih-tih-sc-776623-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=13926653)
[2026-06-03T21:10:25] Marking multi-mapping alignments (marked=9897002)
[2026-06-03T21:10:32] Detecting strandedness (reverse)
[2026-06-03T21:10:32] Assigning strands to alignments 
[2026-06-03T21:10:35] Annotating alignments 
[2026-06-03T21:11:30] Filtering duplicates (remaining=7472398)
[2026-06-03T21:11:40] 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=6786038)
[2026-06-03T21:11:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6786038)
[2026-06-03T21:11:46] Filtering viral contigs with expression lower than the top 5 (remaining=6786038)
[2026-06-03T21:11:53] Filtering viral contigs with less than 5% coverage (remaining=6786038)
[2026-06-03T21:11:57] Estimating fragment length (mate gap mean=-86.9802, mate gap stddev=29.7998, read length mean=126.859)
[2026-06-03T21:11:57] Filtering read-through fragments with a distance <=10000bp (remaining=6548482)
[2026-06-03T21:12:00] Filtering inconsistently clipped mates (remaining=6453094)
[2026-06-03T21:12:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6300402)
[2026-06-03T21:12:10] Filtering fragments with small insert size (remaining=6299324)
[2026-06-03T21:12:13] Filtering alignments with long gaps (remaining=6299324)
[2026-06-03T21:12:17] Filtering fragments with both mates in the same gene (remaining=6297958)
[2026-06-03T21:12:20] Filtering fusions arising from hairpin structures (remaining=5924915)
[2026-06-03T21:12:24] Filtering reads with a mismatch p-value <=0.01 (remaining=1989983)
[2026-06-03T21:12:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=934424)
[2026-06-03T21:12:51] Finding fusions and counting supporting reads (total=721403)
[2026-06-03T21:13:18] Merging adjacent fusion breakpoints (remaining=712533)
[2026-06-03T21:13:20] Filtering multi-mapping fusions by alignment score and read support (remaining=439912)
[2026-06-03T21:14:12] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T21:14:21] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=437266)
[2026-06-03T21:14:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=287245)
[2026-06-03T21:14:23] Filtering fusions with <2 supporting reads (remaining=31546)
[2026-06-03T21:14:24] Filtering fusions with an e-value >=0.3 (remaining=8247)
[2026-06-03T21:14:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8291)
[2026-06-03T21:14:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8140)
[2026-06-03T21:14:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8140)
[2026-06-03T21:14:33] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6102)
[2026-06-03T21:14:40] Searching for fusions with spliced split reads (remaining=6230)
[2026-06-03T21:14:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=4081)
[2026-06-03T21:14:49] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4032)
[2026-06-03T21:14:50] Searching for fusions with >=4 spliced events (remaining=4660)
[2026-06-03T21:14:52] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1820)
[2026-06-03T21:15:06] Filtering fusions with anchors <=23nt (remaining=1252)
[2026-06-03T21:15:07] Filtering end-to-end fusions with low support (remaining=1131)
[2026-06-03T21:15:08] Filtering fusions with no coverage around the breakpoints (remaining=1098)
[2026-06-03T21:15:09] Indexing gene sequences 
[2026-06-03T21:15:15] Filtering genes with >=30% identity (remaining=361)
[2026-06-03T21:15:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=232)
[2026-06-03T21:15:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=184)
[2026-06-03T21:15:23] Searching for additional isoforms (remaining=219)
[2026-06-03T21:15:25] Assigning confidence scores to events 
[2026-06-03T21:15:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T21:15:30] Writing fusions to file 'aih-tih-sc-776623-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T21:15:32] Writing discarded fusions to file 'aih-tih-sc-776623-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T21:16:14] Freeing resources
[2026-06-03T21:16:38] Done (elapsed time=00:13:54, CPU time=00:13:52, peak memory=19.2gb)