[2026-06-08T08:45:22] Launching Arriba 2.4.0
[2026-06-08T08:45:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:45:32] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:45:37] Reading chimeric alignments from 'aih-tih-sc-522d83-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=12139275)
[2026-06-08T08:53:01] Marking multi-mapping alignments (marked=7864981)
[2026-06-08T08:53:06] Detecting strandedness (reverse)
[2026-06-08T08:53:06] Assigning strands to alignments 
[2026-06-08T08:53:09] Annotating alignments 
[2026-06-08T08:53:51] Filtering duplicates (remaining=7506827)
[2026-06-08T08:54:01] 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=7230480)
[2026-06-08T08:54:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7230480)
[2026-06-08T08:54:06] Filtering viral contigs with expression lower than the top 5 (remaining=7230480)
[2026-06-08T08:54:12] Filtering viral contigs with less than 5% coverage (remaining=7230480)
[2026-06-08T08:54:16] Estimating fragment length (mate gap mean=-87.2662, mate gap stddev=29.4837, read length mean=135.057)
[2026-06-08T08:54:16] Filtering read-through fragments with a distance <=10000bp (remaining=6898117)
[2026-06-08T08:54:18] Filtering inconsistently clipped mates (remaining=6806905)
[2026-06-08T08:54:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6680819)
[2026-06-08T08:54:26] Filtering fragments with small insert size (remaining=6680138)
[2026-06-08T08:54:29] Filtering alignments with long gaps (remaining=6680138)
[2026-06-08T08:54:32] Filtering fragments with both mates in the same gene (remaining=6679182)
[2026-06-08T08:54:35] Filtering fusions arising from hairpin structures (remaining=6376744)
[2026-06-08T08:54:39] Filtering reads with a mismatch p-value <=0.01 (remaining=3058769)
[2026-06-08T08:54:57] Filtering reads with low entropy (k-mer content >=60%) (remaining=951040)
[2026-06-08T08:55:09] Finding fusions and counting supporting reads (total=694174)
[2026-06-08T08:55:30] Merging adjacent fusion breakpoints (remaining=688033)
[2026-06-08T08:55:32] Filtering multi-mapping fusions by alignment score and read support (remaining=433002)
[2026-06-08T08:56:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:56:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=430491)
[2026-06-08T08:56:23] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=249996)
[2026-06-08T08:56:24] Filtering fusions with <2 supporting reads (remaining=31258)
[2026-06-08T08:56:25] Filtering fusions with an e-value >=0.3 (remaining=8894)
[2026-06-08T08:56:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8965)
[2026-06-08T08:56:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8861)
[2026-06-08T08:56:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8861)
[2026-06-08T08:56:33] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6887)
[2026-06-08T08:56:39] Searching for fusions with spliced split reads (remaining=6984)
[2026-06-08T08:56:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=4460)
[2026-06-08T08:56:47] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4401)
[2026-06-08T08:56:48] Searching for fusions with >=4 spliced events (remaining=5088)
[2026-06-08T08:56:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1895)
[2026-06-08T08:57:07] Filtering fusions with anchors <=23nt (remaining=1444)
[2026-06-08T08:57:08] Filtering end-to-end fusions with low support (remaining=1408)
[2026-06-08T08:57:09] Filtering fusions with no coverage around the breakpoints (remaining=1377)
[2026-06-08T08:57:10] Indexing gene sequences 
[2026-06-08T08:57:17] Filtering genes with >=30% identity (remaining=448)
[2026-06-08T08:57:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=196)
[2026-06-08T08:57:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=180)
[2026-06-08T08:57:24] Searching for additional isoforms (remaining=224)
[2026-06-08T08:57:26] Assigning confidence scores to events 
[2026-06-08T08:57:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:57:30] Writing fusions to file 'aih-tih-sc-522d83-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:57:32] Writing discarded fusions to file 'aih-tih-sc-522d83-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:58:06] Freeing resources
[2026-06-08T08:58:26] Done (elapsed time=00:13:04, CPU time=00:13:02, peak memory=16.3gb)