[2026-06-08T08:54:23] Launching Arriba 2.4.0
[2026-06-08T08:54:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:54:31] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:54:35] Reading chimeric alignments from 'aih-tih-sc-cab2fc-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9832630)
[2026-06-08T09:02:42] Marking multi-mapping alignments (marked=6117085)
[2026-06-08T09:02:47] Detecting strandedness (reverse)
[2026-06-08T09:02:47] Assigning strands to alignments 
[2026-06-08T09:02:50] Annotating alignments 
[2026-06-08T09:03:29] Filtering duplicates (remaining=6325620)
[2026-06-08T09:03:39] 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=6127292)
[2026-06-08T09:03:41] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6127292)
[2026-06-08T09:03:44] Filtering viral contigs with expression lower than the top 5 (remaining=6127292)
[2026-06-08T09:03:49] Filtering viral contigs with less than 5% coverage (remaining=6127292)
[2026-06-08T09:03:52] Estimating fragment length (mate gap mean=-83.8854, mate gap stddev=31.0526, read length mean=137.089)
[2026-06-08T09:03:52] Filtering read-through fragments with a distance <=10000bp (remaining=5743123)
[2026-06-08T09:03:54] Filtering inconsistently clipped mates (remaining=5647531)
[2026-06-08T09:03:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5520437)
[2026-06-08T09:04:02] Filtering fragments with small insert size (remaining=5519727)
[2026-06-08T09:04:04] Filtering alignments with long gaps (remaining=5519727)
[2026-06-08T09:04:07] Filtering fragments with both mates in the same gene (remaining=5518667)
[2026-06-08T09:04:09] Filtering fusions arising from hairpin structures (remaining=5160793)
[2026-06-08T09:04:12] Filtering reads with a mismatch p-value <=0.01 (remaining=2655205)
[2026-06-08T09:04:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=1121186)
[2026-06-08T09:04:39] Finding fusions and counting supporting reads (total=824060)
[2026-06-08T09:04:58] Merging adjacent fusion breakpoints (remaining=816026)
[2026-06-08T09:05:00] Filtering multi-mapping fusions by alignment score and read support (remaining=531729)
[2026-06-08T09:05:35] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:05:42] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=528014)
[2026-06-08T09:05:43] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=287871)
[2026-06-08T09:05:45] Filtering fusions with <2 supporting reads (remaining=42214)
[2026-06-08T09:05:45] Filtering fusions with an e-value >=0.3 (remaining=17038)
[2026-06-08T09:05:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=17097)
[2026-06-08T09:05:50] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=17002)
[2026-06-08T09:05:51] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=17003)
[2026-06-08T09:05:52] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9648)
[2026-06-08T09:05:57] Searching for fusions with spliced split reads (remaining=9689)
[2026-06-08T09:06:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=4623)
[2026-06-08T09:06:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4541)
[2026-06-08T09:06:04] Searching for fusions with >=4 spliced events (remaining=5724)
[2026-06-08T09:06:06] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2530)
[2026-06-08T09:06:20] Filtering fusions with anchors <=23nt (remaining=2128)
[2026-06-08T09:06:21] Filtering end-to-end fusions with low support (remaining=2076)
[2026-06-08T09:06:22] Filtering fusions with no coverage around the breakpoints (remaining=2044)
[2026-06-08T09:06:22] Indexing gene sequences 
[2026-06-08T09:06:30] Filtering genes with >=30% identity (remaining=862)
[2026-06-08T09:06:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=633)
[2026-06-08T09:07:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=418)
[2026-06-08T09:07:07] Searching for additional isoforms (remaining=579)
[2026-06-08T09:07:08] Assigning confidence scores to events 
[2026-06-08T09:07:11] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:07:12] Writing fusions to file 'aih-tih-sc-cab2fc-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:07:18] Writing discarded fusions to file 'aih-tih-sc-cab2fc-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:07:49] Freeing resources
[2026-06-08T09:08:06] Done (elapsed time=00:13:43, CPU time=00:13:42, peak memory=14.4gb)