[2026-06-03T20:42:45] Launching Arriba 2.4.0
[2026-06-03T20:42:45] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:42:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:42:56] Reading chimeric alignments from 'aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10263574)
[2026-06-03T20:49:49] Marking multi-mapping alignments (marked=6796664)
[2026-06-03T20:49:53] Detecting strandedness (reverse)
[2026-06-03T20:49:53] Assigning strands to alignments 
[2026-06-03T20:49:55] Annotating alignments 
[2026-06-03T20:50:28] Filtering duplicates (remaining=6975293)
[2026-06-03T20:50:36] 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=6668109)
[2026-06-03T20:50:39] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6668109)
[2026-06-03T20:50:41] Filtering viral contigs with expression lower than the top 5 (remaining=6668109)
[2026-06-03T20:50:46] Filtering viral contigs with less than 5% coverage (remaining=6668109)
[2026-06-03T20:50:49] Estimating fragment length (mate gap mean=-83.0392, mate gap stddev=29.7986, read length mean=130.574)
[2026-06-03T20:50:49] Filtering read-through fragments with a distance <=10000bp (remaining=6214032)
[2026-06-03T20:50:51] Filtering inconsistently clipped mates (remaining=6102763)
[2026-06-03T20:50:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5961729)
[2026-06-03T20:50:58] Filtering fragments with small insert size (remaining=5960814)
[2026-06-03T20:51:01] Filtering alignments with long gaps (remaining=5960814)
[2026-06-03T20:51:03] Filtering fragments with both mates in the same gene (remaining=5959734)
[2026-06-03T20:51:05] Filtering fusions arising from hairpin structures (remaining=5543707)
[2026-06-03T20:51:08] Filtering reads with a mismatch p-value <=0.01 (remaining=2579829)
[2026-06-03T20:51:22] Filtering reads with low entropy (k-mer content >=60%) (remaining=1218428)
[2026-06-03T20:51:33] Finding fusions and counting supporting reads (total=894816)
[2026-06-03T20:51:48] Merging adjacent fusion breakpoints (remaining=885052)
[2026-06-03T20:51:50] Filtering multi-mapping fusions by alignment score and read support (remaining=551586)
[2026-06-03T20:52:19] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:52:27] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=548777)
[2026-06-03T20:52:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=320708)
[2026-06-03T20:52:28] Filtering fusions with <2 supporting reads (remaining=36801)
[2026-06-03T20:52:29] Filtering fusions with an e-value >=0.3 (remaining=10465)
[2026-06-03T20:52:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10527)
[2026-06-03T20:52:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10454)
[2026-06-03T20:52:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10454)
[2026-06-03T20:52:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8242)
[2026-06-03T20:52:41] Searching for fusions with spliced split reads (remaining=8368)
[2026-06-03T20:52:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=4567)
[2026-06-03T20:52:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4522)
[2026-06-03T20:52:48] Searching for fusions with >=4 spliced events (remaining=5329)
[2026-06-03T20:52:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1825)
[2026-06-03T20:53:04] Filtering fusions with anchors <=23nt (remaining=1423)
[2026-06-03T20:53:05] Filtering end-to-end fusions with low support (remaining=1397)
[2026-06-03T20:53:06] Filtering fusions with no coverage around the breakpoints (remaining=1365)
[2026-06-03T20:53:06] Indexing gene sequences 
[2026-06-03T20:53:12] Filtering genes with >=30% identity (remaining=431)
[2026-06-03T20:53:14] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=168)
[2026-06-03T20:53:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=157)
[2026-06-03T20:53:19] Searching for additional isoforms (remaining=204)
[2026-06-03T20:53:20] Assigning confidence scores to events 
[2026-06-03T20:53:23] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:53:23] Writing fusions to file 'aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:53:25] Writing discarded fusions to file 'aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:53:52] Freeing resources
[2026-06-03T20:54:09] Done (elapsed time=00:11:24, CPU time=00:11:23, peak memory=14.9gb)