[2026-06-08T09:00:21] Launching Arriba 2.4.0
[2026-06-08T09:00:21] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:00:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:00:34] Reading chimeric alignments from 'aih-tih-sc-656590-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9581119)
[2026-06-08T09:06:51] Marking multi-mapping alignments (marked=6382352)
[2026-06-08T09:06:55] Detecting strandedness (reverse)
[2026-06-08T09:06:55] Assigning strands to alignments 
[2026-06-08T09:06:57] Annotating alignments 
[2026-06-08T09:07:28] Filtering duplicates (remaining=6500915)
[2026-06-08T09:07:36] 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=6097864)
[2026-06-08T09:07:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6097864)
[2026-06-08T09:07:39] Filtering viral contigs with expression lower than the top 5 (remaining=6097864)
[2026-06-08T09:07:44] Filtering viral contigs with less than 5% coverage (remaining=6097864)
[2026-06-08T09:07:46] Estimating fragment length (mate gap mean=-84.98, mate gap stddev=29.1109, read length mean=128.926)
[2026-06-08T09:07:46] Filtering read-through fragments with a distance <=10000bp (remaining=5742421)
[2026-06-08T09:07:48] Filtering inconsistently clipped mates (remaining=5613690)
[2026-06-08T09:07:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5465699)
[2026-06-08T09:07:55] Filtering fragments with small insert size (remaining=5464851)
[2026-06-08T09:07:56] Filtering alignments with long gaps (remaining=5464850)
[2026-06-08T09:07:58] Filtering fragments with both mates in the same gene (remaining=5463734)
[2026-06-08T09:08:00] Filtering fusions arising from hairpin structures (remaining=5063590)
[2026-06-08T09:08:03] Filtering reads with a mismatch p-value <=0.01 (remaining=2170990)
[2026-06-08T09:08:16] Filtering reads with low entropy (k-mer content >=60%) (remaining=1033530)
[2026-06-08T09:08:27] Finding fusions and counting supporting reads (total=805729)
[2026-06-08T09:08:44] Merging adjacent fusion breakpoints (remaining=799008)
[2026-06-08T09:08:45] Filtering multi-mapping fusions by alignment score and read support (remaining=504305)
[2026-06-08T09:09:17] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:09:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=502615)
[2026-06-08T09:09:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=301974)
[2026-06-08T09:09:26] Filtering fusions with <2 supporting reads (remaining=32083)
[2026-06-08T09:09:27] Filtering fusions with an e-value >=0.3 (remaining=8487)
[2026-06-08T09:09:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8554)
[2026-06-08T09:09:31] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8462)
[2026-06-08T09:09:32] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8462)
[2026-06-08T09:09:34] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6043)
[2026-06-08T09:09:39] Searching for fusions with spliced split reads (remaining=6069)
[2026-06-08T09:09:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=3845)
[2026-06-08T09:09:45] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3817)
[2026-06-08T09:09:46] Searching for fusions with >=4 spliced events (remaining=4753)
[2026-06-08T09:09:47] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2127)
[2026-06-08T09:10:02] Filtering fusions with anchors <=23nt (remaining=1715)
[2026-06-08T09:10:03] Filtering end-to-end fusions with low support (remaining=1656)
[2026-06-08T09:10:04] Filtering fusions with no coverage around the breakpoints (remaining=1626)
[2026-06-08T09:10:04] Indexing gene sequences 
[2026-06-08T09:10:11] Filtering genes with >=30% identity (remaining=511)
[2026-06-08T09:10:14] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=230)
[2026-06-08T09:10:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=175)
[2026-06-08T09:10:19] Searching for additional isoforms (remaining=228)
[2026-06-08T09:10:21] Assigning confidence scores to events 
[2026-06-08T09:10:24] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:10:25] Writing fusions to file 'aih-tih-sc-656590-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:10:26] Writing discarded fusions to file 'aih-tih-sc-656590-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:10:58] Freeing resources
[2026-06-08T09:11:14] Done (elapsed time=00:10:53, CPU time=00:10:51, peak memory=14.3gb)