[2026-06-03T20:17:01] Launching Arriba 2.4.0
[2026-06-03T20:17:01] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:17:09] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:17:13] Reading chimeric alignments from 'aih-tih-sc-f27606-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=14728773)
[2026-06-03T20:24:00] Marking multi-mapping alignments (marked=10964119)
[2026-06-03T20:24:06] Detecting strandedness (reverse)
[2026-06-03T20:24:06] Assigning strands to alignments 
[2026-06-03T20:24:09] Annotating alignments 
[2026-06-03T20:24:55] Filtering duplicates (remaining=4539427)
[2026-06-03T20:25:02] 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=3944403)
[2026-06-03T20:25:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3944403)
[2026-06-03T20:25:08] Filtering viral contigs with expression lower than the top 5 (remaining=3944403)
[2026-06-03T20:25:14] Filtering viral contigs with less than 5% coverage (remaining=3944403)
[2026-06-03T20:25:17] Estimating fragment length (mate gap mean=-83.3158, mate gap stddev=28.5927, read length mean=119.319)
[2026-06-03T20:25:17] Filtering read-through fragments with a distance <=10000bp (remaining=3787572)
[2026-06-03T20:25:19] Filtering inconsistently clipped mates (remaining=3687628)
[2026-06-03T20:25:22] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3494850)
[2026-06-03T20:25:26] Filtering fragments with small insert size (remaining=3493354)
[2026-06-03T20:25:29] Filtering alignments with long gaps (remaining=3493354)
[2026-06-03T20:25:32] Filtering fragments with both mates in the same gene (remaining=3492338)
[2026-06-03T20:25:34] Filtering fusions arising from hairpin structures (remaining=3288702)
[2026-06-03T20:25:37] Filtering reads with a mismatch p-value <=0.01 (remaining=1187281)
[2026-06-03T20:25:47] Filtering reads with low entropy (k-mer content >=60%) (remaining=407476)
[2026-06-03T20:25:55] Finding fusions and counting supporting reads (total=352340)
[2026-06-03T20:26:14] Merging adjacent fusion breakpoints (remaining=349049)
[2026-06-03T20:26:15] Filtering multi-mapping fusions by alignment score and read support (remaining=178256)
[2026-06-03T20:26:57] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:27:03] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=176873)
[2026-06-03T20:27:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=110728)
[2026-06-03T20:27:04] Filtering fusions with <2 supporting reads (remaining=8643)
[2026-06-03T20:27:04] Filtering fusions with an e-value >=0.3 (remaining=2137)
[2026-06-03T20:27:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2169)
[2026-06-03T20:27:09] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2079)
[2026-06-03T20:27:09] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2079)
[2026-06-03T20:27:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2038)
[2026-06-03T20:27:16] Searching for fusions with spliced split reads (remaining=2095)
[2026-06-03T20:27:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=1532)
[2026-06-03T20:27:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1513)
[2026-06-03T20:27:23] Searching for fusions with >=4 spliced events (remaining=1700)
[2026-06-03T20:27:24] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=665)
[2026-06-03T20:27:36] Filtering fusions with anchors <=23nt (remaining=520)
[2026-06-03T20:27:37] Filtering end-to-end fusions with low support (remaining=499)
[2026-06-03T20:27:37] Filtering fusions with no coverage around the breakpoints (remaining=490)
[2026-06-03T20:27:38] Indexing gene sequences 
[2026-06-03T20:27:41] Filtering genes with >=30% identity (remaining=137)
[2026-06-03T20:27:42] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=54)
[2026-06-03T20:27:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=54)
[2026-06-03T20:27:44] Searching for additional isoforms (remaining=72)
[2026-06-03T20:27:45] Assigning confidence scores to events 
[2026-06-03T20:27:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:27:48] Writing fusions to file 'aih-tih-sc-f27606-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:27:49] Writing discarded fusions to file 'aih-tih-sc-f27606-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:28:09] Freeing resources
[2026-06-03T20:28:29] Done (elapsed time=00:11:28, CPU time=00:11:27, peak memory=19.4gb)