[2026-06-03T20:15:48] Launching Arriba 2.4.0
[2026-06-03T20:15:48] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:15:56] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:16:00] Reading chimeric alignments from 'aih-tih-sc-ffabe0-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10124387)
[2026-06-03T20:22:29] Marking multi-mapping alignments (marked=6595874)
[2026-06-03T20:22:34] Detecting strandedness (reverse)
[2026-06-03T20:22:34] Assigning strands to alignments 
[2026-06-03T20:22:36] Annotating alignments 
[2026-06-03T20:23:11] Filtering duplicates (remaining=5924728)
[2026-06-03T20:23:17] 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=5613279)
[2026-06-03T20:23:19] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5613279)
[2026-06-03T20:23:21] Filtering viral contigs with expression lower than the top 5 (remaining=5613279)
[2026-06-03T20:23:25] Filtering viral contigs with less than 5% coverage (remaining=5613279)
[2026-06-03T20:23:28] Estimating fragment length (mate gap mean=-84.114, mate gap stddev=28.5092, read length mean=125.293)
[2026-06-03T20:23:28] Filtering read-through fragments with a distance <=10000bp (remaining=5313199)
[2026-06-03T20:23:30] Filtering inconsistently clipped mates (remaining=5189917)
[2026-06-03T20:23:32] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5010362)
[2026-06-03T20:23:36] Filtering fragments with small insert size (remaining=5009172)
[2026-06-03T20:23:38] Filtering alignments with long gaps (remaining=5009172)
[2026-06-03T20:23:40] Filtering fragments with both mates in the same gene (remaining=5007988)
[2026-06-03T20:23:42] Filtering fusions arising from hairpin structures (remaining=4646150)
[2026-06-03T20:23:45] Filtering reads with a mismatch p-value <=0.01 (remaining=1955921)
[2026-06-03T20:23:57] Filtering reads with low entropy (k-mer content >=60%) (remaining=896777)
[2026-06-03T20:24:06] Finding fusions and counting supporting reads (total=693562)
[2026-06-03T20:24:22] Merging adjacent fusion breakpoints (remaining=686956)
[2026-06-03T20:24:23] Filtering multi-mapping fusions by alignment score and read support (remaining=421575)
[2026-06-03T20:24:55] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:25:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=420008)
[2026-06-03T20:25:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=240673)
[2026-06-03T20:25:03] Filtering fusions with <2 supporting reads (remaining=28874)
[2026-06-03T20:25:04] Filtering fusions with an e-value >=0.3 (remaining=7192)
[2026-06-03T20:25:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7257)
[2026-06-03T20:25:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7168)
[2026-06-03T20:25:09] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7168)
[2026-06-03T20:25:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6409)
[2026-06-03T20:25:15] Searching for fusions with spliced split reads (remaining=6525)
[2026-06-03T20:25:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=4317)
[2026-06-03T20:25:21] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4256)
[2026-06-03T20:25:22] Searching for fusions with >=4 spliced events (remaining=4957)
[2026-06-03T20:25:23] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1701)
[2026-06-03T20:25:37] Filtering fusions with anchors <=23nt (remaining=1395)
[2026-06-03T20:25:38] Filtering end-to-end fusions with low support (remaining=1353)
[2026-06-03T20:25:39] Filtering fusions with no coverage around the breakpoints (remaining=1327)
[2026-06-03T20:25:39] Indexing gene sequences 
[2026-06-03T20:25:44] Filtering genes with >=30% identity (remaining=387)
[2026-06-03T20:25:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=177)
[2026-06-03T20:25:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=166)
[2026-06-03T20:25:51] Searching for additional isoforms (remaining=205)
[2026-06-03T20:25:52] Assigning confidence scores to events 
[2026-06-03T20:25:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:25:56] Writing fusions to file 'aih-tih-sc-ffabe0-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:25:57] Writing discarded fusions to file 'aih-tih-sc-ffabe0-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:26:24] Freeing resources
[2026-06-03T20:26:40] Done (elapsed time=00:10:52, CPU time=00:10:51, peak memory=14.7gb)