[2026-06-03T20:28:45] Launching Arriba 2.4.0
[2026-06-03T20:28:45] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:28:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:28:58] Reading chimeric alignments from 'aih-tih-sc-01eb49-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11028199)
[2026-06-03T20:36:52] Marking multi-mapping alignments (marked=7234653)
[2026-06-03T20:36:58] Detecting strandedness (reverse)
[2026-06-03T20:36:58] Assigning strands to alignments 
[2026-06-03T20:37:01] Annotating alignments 
[2026-06-03T20:37:44] Filtering duplicates (remaining=7389892)
[2026-06-03T20:37:54] 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=6902516)
[2026-06-03T20:37:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6902516)
[2026-06-03T20:37:59] Filtering viral contigs with expression lower than the top 5 (remaining=6902516)
[2026-06-03T20:38:05] Filtering viral contigs with less than 5% coverage (remaining=6902516)
[2026-06-03T20:38:08] Estimating fragment length (mate gap mean=-82.198, mate gap stddev=32.5689, read length mean=131.357)
[2026-06-03T20:38:08] Filtering read-through fragments with a distance <=10000bp (remaining=6555750)
[2026-06-03T20:38:11] Filtering inconsistently clipped mates (remaining=6430806)
[2026-06-03T20:38:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6262960)
[2026-06-03T20:38:20] Filtering fragments with small insert size (remaining=6262102)
[2026-06-03T20:38:23] Filtering alignments with long gaps (remaining=6262102)
[2026-06-03T20:38:26] Filtering fragments with both mates in the same gene (remaining=6260785)
[2026-06-03T20:38:29] Filtering fusions arising from hairpin structures (remaining=5858270)
[2026-06-03T20:38:33] Filtering reads with a mismatch p-value <=0.01 (remaining=2589611)
[2026-06-03T20:38:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=1206528)
[2026-06-03T20:39:01] Finding fusions and counting supporting reads (total=844030)
[2026-06-03T20:39:25] Merging adjacent fusion breakpoints (remaining=832872)
[2026-06-03T20:39:27] Filtering multi-mapping fusions by alignment score and read support (remaining=548104)
[2026-06-03T20:40:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:40:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=545559)
[2026-06-03T20:40:21] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=324025)
[2026-06-03T20:40:23] Filtering fusions with <2 supporting reads (remaining=56760)
[2026-06-03T20:40:24] Filtering fusions with an e-value >=0.3 (remaining=24136)
[2026-06-03T20:40:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=24204)
[2026-06-03T20:40:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=24091)
[2026-06-03T20:40:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=24091)
[2026-06-03T20:40:32] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9696)
[2026-06-03T20:40:39] Searching for fusions with spliced split reads (remaining=9745)
[2026-06-03T20:40:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=4736)
[2026-06-03T20:40:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4673)
[2026-06-03T20:40:49] Searching for fusions with >=4 spliced events (remaining=5715)
[2026-06-03T20:40:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2092)
[2026-06-03T20:41:09] Filtering fusions with anchors <=23nt (remaining=1619)
[2026-06-03T20:41:10] Filtering end-to-end fusions with low support (remaining=1554)
[2026-06-03T20:41:10] Filtering fusions with no coverage around the breakpoints (remaining=1530)
[2026-06-03T20:41:11] Indexing gene sequences 
[2026-06-03T20:41:18] Filtering genes with >=30% identity (remaining=447)
[2026-06-03T20:41:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=210)
[2026-06-03T20:41:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=186)
[2026-06-03T20:41:27] Searching for additional isoforms (remaining=243)
[2026-06-03T20:41:29] Assigning confidence scores to events 
[2026-06-03T20:41:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:41:33] Writing fusions to file 'aih-tih-sc-01eb49-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:41:35] Writing discarded fusions to file 'aih-tih-sc-01eb49-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:42:18] Freeing resources
[2026-06-03T20:42:41] Done (elapsed time=00:13:56, CPU time=00:13:54, peak memory=15.9gb)