[2026-06-03T19:42:21] Launching Arriba 2.4.0
[2026-06-03T19:42:21] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:42:35] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:42:40] Reading chimeric alignments from 'aih-tih-sc-790e56-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=6221485)
[2026-06-03T19:48:13] Marking multi-mapping alignments (marked=4111656)
[2026-06-03T19:48:17] Detecting strandedness (reverse)
[2026-06-03T19:48:17] Assigning strands to alignments 
[2026-06-03T19:48:18] Annotating alignments 
[2026-06-03T19:48:44] Filtering duplicates (remaining=4495730)
[2026-06-03T19:48:50] 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=4227022)
[2026-06-03T19:48:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4227022)
[2026-06-03T19:48:52] Filtering viral contigs with expression lower than the top 5 (remaining=4227022)
[2026-06-03T19:48:56] Filtering viral contigs with less than 5% coverage (remaining=4227022)
[2026-06-03T19:48:57] Estimating fragment length (mate gap mean=-85.4544, mate gap stddev=29.3686, read length mean=128.164)
[2026-06-03T19:48:58] Filtering read-through fragments with a distance <=10000bp (remaining=3973717)
[2026-06-03T19:48:59] Filtering inconsistently clipped mates (remaining=3885339)
[2026-06-03T19:49:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3766998)
[2026-06-03T19:49:04] Filtering fragments with small insert size (remaining=3766391)
[2026-06-03T19:49:05] Filtering alignments with long gaps (remaining=3766391)
[2026-06-03T19:49:07] Filtering fragments with both mates in the same gene (remaining=3765568)
[2026-06-03T19:49:09] Filtering fusions arising from hairpin structures (remaining=3494746)
[2026-06-03T19:49:11] Filtering reads with a mismatch p-value <=0.01 (remaining=1520257)
[2026-06-03T19:49:21] Filtering reads with low entropy (k-mer content >=60%) (remaining=744865)
[2026-06-03T19:49:30] Finding fusions and counting supporting reads (total=609254)
[2026-06-03T19:49:45] Merging adjacent fusion breakpoints (remaining=603883)
[2026-06-03T19:49:46] Filtering multi-mapping fusions by alignment score and read support (remaining=367725)
[2026-06-03T19:50:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T19:50:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=366034)
[2026-06-03T19:50:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=224995)
[2026-06-03T19:50:19] Filtering fusions with <2 supporting reads (remaining=26811)
[2026-06-03T19:50:19] Filtering fusions with an e-value >=0.3 (remaining=9385)
[2026-06-03T19:50:20] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9448)
[2026-06-03T19:50:23] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9406)
[2026-06-03T19:50:23] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9406)
[2026-06-03T19:50:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4787)
[2026-06-03T19:50:28] Searching for fusions with spliced split reads (remaining=4889)
[2026-06-03T19:50:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=3307)
[2026-06-03T19:50:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3250)
[2026-06-03T19:50:34] Searching for fusions with >=4 spliced events (remaining=3770)
[2026-06-03T19:50:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1415)
[2026-06-03T19:50:51] Filtering fusions with anchors <=23nt (remaining=1096)
[2026-06-03T19:50:51] Filtering end-to-end fusions with low support (remaining=1060)
[2026-06-03T19:50:52] Filtering fusions with no coverage around the breakpoints (remaining=1032)
[2026-06-03T19:50:53] Indexing gene sequences 
[2026-06-03T19:50:58] Filtering genes with >=30% identity (remaining=361)
[2026-06-03T19:51:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=218)
[2026-06-03T19:51:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=179)
[2026-06-03T19:51:05] Searching for additional isoforms (remaining=211)
[2026-06-03T19:51:06] Assigning confidence scores to events 
[2026-06-03T19:51:10] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T19:51:10] Writing fusions to file 'aih-tih-sc-790e56-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T19:51:12] Writing discarded fusions to file 'aih-tih-sc-790e56-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T19:51:45] Freeing resources
[2026-06-03T19:52:04] Done (elapsed time=00:09:43, CPU time=00:09:41, peak memory=10.9gb)