[2026-06-03T19:55:37] Launching Arriba 2.4.0
[2026-06-03T19:55:37] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:55:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:56:00] Reading chimeric alignments from 'aih-tih-sc-f834a3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9276524)
[2026-06-03T20:04:54] Marking multi-mapping alignments (marked=6345010)
[2026-06-03T20:05:00] Detecting strandedness (reverse)
[2026-06-03T20:05:00] Assigning strands to alignments 
[2026-06-03T20:05:03] Annotating alignments 
[2026-06-03T20:05:57] Filtering duplicates (remaining=5002557)
[2026-06-03T20:06:08] 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=4666439)
[2026-06-03T20:06:10] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4666439)
[2026-06-03T20:06:13] Filtering viral contigs with expression lower than the top 5 (remaining=4666439)
[2026-06-03T20:06:19] Filtering viral contigs with less than 5% coverage (remaining=4666439)
[2026-06-03T20:06:22] Estimating fragment length (mate gap mean=-84.2853, mate gap stddev=29.2565, read length mean=125.314)
[2026-06-03T20:06:22] Filtering read-through fragments with a distance <=10000bp (remaining=4449670)
[2026-06-03T20:06:26] Filtering inconsistently clipped mates (remaining=4328436)
[2026-06-03T20:06:29] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4134927)
[2026-06-03T20:06:34] Filtering fragments with small insert size (remaining=4133884)
[2026-06-03T20:06:37] Filtering alignments with long gaps (remaining=4133884)
[2026-06-03T20:06:40] Filtering fragments with both mates in the same gene (remaining=4132739)
[2026-06-03T20:06:43] Filtering fusions arising from hairpin structures (remaining=3782299)
[2026-06-03T20:06:46] Filtering reads with a mismatch p-value <=0.01 (remaining=1567980)
[2026-06-03T20:07:00] Filtering reads with low entropy (k-mer content >=60%) (remaining=695895)
[2026-06-03T20:07:12] Finding fusions and counting supporting reads (total=568747)
[2026-06-03T20:07:36] Merging adjacent fusion breakpoints (remaining=563135)
[2026-06-03T20:07:38] Filtering multi-mapping fusions by alignment score and read support (remaining=324953)
[2026-06-03T20:08:31] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:08:43] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=322203)
[2026-06-03T20:08:43] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=205781)
[2026-06-03T20:08:45] Filtering fusions with <2 supporting reads (remaining=22757)
[2026-06-03T20:08:46] Filtering fusions with an e-value >=0.3 (remaining=6223)
[2026-06-03T20:08:47] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6283)
[2026-06-03T20:08:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6120)
[2026-06-03T20:08:52] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6120)
[2026-06-03T20:08:54] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4520)
[2026-06-03T20:09:03] Searching for fusions with spliced split reads (remaining=4535)
[2026-06-03T20:09:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=3057)
[2026-06-03T20:09:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3018)
[2026-06-03T20:09:12] Searching for fusions with >=4 spliced events (remaining=3569)
[2026-06-03T20:09:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1311)
[2026-06-03T20:09:44] Filtering fusions with anchors <=23nt (remaining=1091)
[2026-06-03T20:09:45] Filtering end-to-end fusions with low support (remaining=1047)
[2026-06-03T20:09:46] Filtering fusions with no coverage around the breakpoints (remaining=1015)
[2026-06-03T20:09:46] Indexing gene sequences 
[2026-06-03T20:09:59] Filtering genes with >=30% identity (remaining=363)
[2026-06-03T20:10:04] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=205)
[2026-06-03T20:10:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=185)
[2026-06-03T20:10:09] Searching for additional isoforms (remaining=242)
[2026-06-03T20:10:10] Assigning confidence scores to events 
[2026-06-03T20:10:15] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:10:15] Writing fusions to file 'aih-tih-sc-f834a3-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:10:18] Writing discarded fusions to file 'aih-tih-sc-f834a3-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:10:59] Freeing resources
[2026-06-03T20:11:28] Done (elapsed time=00:15:51, CPU time=00:15:49, peak memory=14gb)