[2026-06-03T19:35:44] Launching Arriba 2.4.0
[2026-06-03T19:35:44] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:35:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:35:57] Reading chimeric alignments from 'aih-tih-sc-8e3550-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=5582380)
[2026-06-03T19:39:51] Marking multi-mapping alignments (marked=3712244)
[2026-06-03T19:39:54] Detecting strandedness (reverse)
[2026-06-03T19:39:54] Assigning strands to alignments 
[2026-06-03T19:39:55] Annotating alignments 
[2026-06-03T19:40:21] Filtering duplicates (remaining=4045206)
[2026-06-03T19:40:27] 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=3822895)
[2026-06-03T19:40:29] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3822895)
[2026-06-03T19:40:31] Filtering viral contigs with expression lower than the top 5 (remaining=3822895)
[2026-06-03T19:40:35] Filtering viral contigs with less than 5% coverage (remaining=3822895)
[2026-06-03T19:40:37] Estimating fragment length (mate gap mean=-83.9201, mate gap stddev=30.7027, read length mean=132.036)
[2026-06-03T19:40:37] Filtering read-through fragments with a distance <=10000bp (remaining=3626114)
[2026-06-03T19:40:39] Filtering inconsistently clipped mates (remaining=3554722)
[2026-06-03T19:40:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3459465)
[2026-06-03T19:40:45] Filtering fragments with small insert size (remaining=3458949)
[2026-06-03T19:40:47] Filtering alignments with long gaps (remaining=3458949)
[2026-06-03T19:40:49] Filtering fragments with both mates in the same gene (remaining=3458266)
[2026-06-03T19:40:51] Filtering fusions arising from hairpin structures (remaining=3208671)
[2026-06-03T19:40:53] Filtering reads with a mismatch p-value <=0.01 (remaining=1522249)
[2026-06-03T19:41:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=690035)
[2026-06-03T19:41:12] Finding fusions and counting supporting reads (total=558816)
[2026-06-03T19:41:27] Merging adjacent fusion breakpoints (remaining=555506)
[2026-06-03T19:41:29] Filtering multi-mapping fusions by alignment score and read support (remaining=342526)
[2026-06-03T19:41:59] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T19:42:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=340801)
[2026-06-03T19:42:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=210429)
[2026-06-03T19:42:09] Filtering fusions with <2 supporting reads (remaining=22597)
[2026-06-03T19:42:09] Filtering fusions with an e-value >=0.3 (remaining=7984)
[2026-06-03T19:42:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8031)
[2026-06-03T19:42:13] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7956)
[2026-06-03T19:42:14] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7956)
[2026-06-03T19:42:16] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5361)
[2026-06-03T19:42:20] Searching for fusions with spliced split reads (remaining=5467)
[2026-06-03T19:42:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=3010)
[2026-06-03T19:42:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2971)
[2026-06-03T19:42:28] Searching for fusions with >=4 spliced events (remaining=3625)
[2026-06-03T19:42:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1571)
[2026-06-03T19:42:51] Filtering fusions with anchors <=23nt (remaining=1322)
[2026-06-03T19:42:52] Filtering end-to-end fusions with low support (remaining=1299)
[2026-06-03T19:42:52] Filtering fusions with no coverage around the breakpoints (remaining=1273)
[2026-06-03T19:42:53] Indexing gene sequences 
[2026-06-03T19:43:03] Filtering genes with >=30% identity (remaining=564)
[2026-06-03T19:43:09] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=390)
[2026-06-03T19:43:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=271)
[2026-06-03T19:43:16] Searching for additional isoforms (remaining=367)
[2026-06-03T19:43:18] Assigning confidence scores to events 
[2026-06-03T19:43:22] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T19:43:22] Writing fusions to file 'aih-tih-sc-8e3550-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T19:43:26] Writing discarded fusions to file 'aih-tih-sc-8e3550-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T19:44:01] Freeing resources
[2026-06-03T19:44:20] Done (elapsed time=00:08:36, CPU time=00:08:35, peak memory=10.1gb)