[2026-06-08T08:14:51] Launching Arriba 2.4.0
[2026-06-08T08:14:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:15:08] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:15:12] Reading chimeric alignments from 'aih-tih-sc-41b5f1-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=6260727)
[2026-06-08T08:18:49] Marking multi-mapping alignments (marked=4478886)
[2026-06-08T08:18:52] Detecting strandedness (reverse)
[2026-06-08T08:18:52] Assigning strands to alignments 
[2026-06-08T08:18:53] Annotating alignments 
[2026-06-08T08:19:18] Filtering duplicates (remaining=1781680)
[2026-06-08T08:19:21] 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=1586275)
[2026-06-08T08:19:23] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1586275)
[2026-06-08T08:19:24] Filtering viral contigs with expression lower than the top 5 (remaining=1586275)
[2026-06-08T08:19:27] Filtering viral contigs with less than 5% coverage (remaining=1586275)
[2026-06-08T08:19:28] Estimating fragment length (mate gap mean=-85.8984, mate gap stddev=28.0002, read length mean=122.972)
[2026-06-08T08:19:29] Filtering read-through fragments with a distance <=10000bp (remaining=1532211)
[2026-06-08T08:19:30] Filtering inconsistently clipped mates (remaining=1499076)
[2026-06-08T08:19:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1436035)
[2026-06-08T08:19:33] Filtering fragments with small insert size (remaining=1435619)
[2026-06-08T08:19:35] Filtering alignments with long gaps (remaining=1435619)
[2026-06-08T08:19:36] Filtering fragments with both mates in the same gene (remaining=1435268)
[2026-06-08T08:19:37] Filtering fusions arising from hairpin structures (remaining=1364667)
[2026-06-08T08:19:39] Filtering reads with a mismatch p-value <=0.01 (remaining=484095)
[2026-06-08T08:19:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=159803)
[2026-06-08T08:19:47] Finding fusions and counting supporting reads (total=146319)
[2026-06-08T08:19:58] Merging adjacent fusion breakpoints (remaining=145450)
[2026-06-08T08:19:58] Filtering multi-mapping fusions by alignment score and read support (remaining=75411)
[2026-06-08T08:20:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:20:23] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=74834)
[2026-06-08T08:20:23] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=48666)
[2026-06-08T08:20:24] Filtering fusions with <2 supporting reads (remaining=3212)
[2026-06-08T08:20:24] Filtering fusions with an e-value >=0.3 (remaining=795)
[2026-06-08T08:20:24] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=813)
[2026-06-08T08:20:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=787)
[2026-06-08T08:20:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=787)
[2026-06-08T08:20:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=777)
[2026-06-08T08:20:29] Searching for fusions with spliced split reads (remaining=841)
[2026-06-08T08:20:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=669)
[2026-06-08T08:20:32] Filtering read-through fusions with breakpoints near the gene boundary (remaining=659)
[2026-06-08T08:20:33] Searching for fusions with >=4 spliced events (remaining=710)
[2026-06-08T08:20:33] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=189)
[2026-06-08T08:20:49] Filtering fusions with anchors <=23nt (remaining=143)
[2026-06-08T08:20:49] Filtering end-to-end fusions with low support (remaining=132)
[2026-06-08T08:20:50] Filtering fusions with no coverage around the breakpoints (remaining=126)
[2026-06-08T08:20:50] Indexing gene sequences 
[2026-06-08T08:20:52] Filtering genes with >=30% identity (remaining=38)
[2026-06-08T08:20:52] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=19)
[2026-06-08T08:20:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=19)
[2026-06-08T08:20:53] Searching for additional isoforms (remaining=21)
[2026-06-08T08:20:53] Assigning confidence scores to events 
[2026-06-08T08:20:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:20:55] Writing fusions to file 'aih-tih-sc-41b5f1-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:20:55] Writing discarded fusions to file 'aih-tih-sc-41b5f1-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:21:08] Freeing resources
[2026-06-08T08:21:20] Done (elapsed time=00:06:29, CPU time=00:06:28, peak memory=10.6gb)