[2026-06-08T08:42:18] Launching Arriba 2.4.0
[2026-06-08T08:42:18] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:42:26] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:42:30] Reading chimeric alignments from 'aih-tih-sc-d666f1-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=14059601)
[2026-06-08T08:48:43] Marking multi-mapping alignments (marked=10504486)
[2026-06-08T08:48:49] Detecting strandedness (reverse)
[2026-06-08T08:48:49] Assigning strands to alignments 
[2026-06-08T08:48:52] Annotating alignments 
[2026-06-08T08:49:40] Filtering duplicates (remaining=6037182)
[2026-06-08T08:49:48] 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=5204713)
[2026-06-08T08:49:50] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5204713)
[2026-06-08T08:49:53] Filtering viral contigs with expression lower than the top 5 (remaining=5204713)
[2026-06-08T08:49:58] Filtering viral contigs with less than 5% coverage (remaining=5204713)
[2026-06-08T08:50:01] Estimating fragment length (mate gap mean=-77.6825, mate gap stddev=29.0731, read length mean=110.3)
[2026-06-08T08:50:01] Filtering read-through fragments with a distance <=10000bp (remaining=4983736)
[2026-06-08T08:50:04] Filtering inconsistently clipped mates (remaining=4867195)
[2026-06-08T08:50:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4668601)
[2026-06-08T08:50:11] Filtering fragments with small insert size (remaining=4666627)
[2026-06-08T08:50:13] Filtering alignments with long gaps (remaining=4666627)
[2026-06-08T08:50:16] Filtering fragments with both mates in the same gene (remaining=4665284)
[2026-06-08T08:50:18] Filtering fusions arising from hairpin structures (remaining=4381268)
[2026-06-08T08:50:21] Filtering reads with a mismatch p-value <=0.01 (remaining=1358264)
[2026-06-08T08:50:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=591968)
[2026-06-08T08:50:40] Finding fusions and counting supporting reads (total=521873)
[2026-06-08T08:51:00] Merging adjacent fusion breakpoints (remaining=513427)
[2026-06-08T08:51:01] Filtering multi-mapping fusions by alignment score and read support (remaining=273578)
[2026-06-08T08:51:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:51:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=272081)
[2026-06-08T08:51:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=170779)
[2026-06-08T08:51:52] Filtering fusions with <2 supporting reads (remaining=14082)
[2026-06-08T08:51:53] Filtering fusions with an e-value >=0.3 (remaining=3341)
[2026-06-08T08:51:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3388)
[2026-06-08T08:51:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3305)
[2026-06-08T08:51:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3305)
[2026-06-08T08:52:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3282)
[2026-06-08T08:52:06] Searching for fusions with spliced split reads (remaining=3341)
[2026-06-08T08:52:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=2386)
[2026-06-08T08:52:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2368)
[2026-06-08T08:52:14] Searching for fusions with >=4 spliced events (remaining=2668)
[2026-06-08T08:52:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1218)
[2026-06-08T08:52:31] Filtering fusions with anchors <=23nt (remaining=842)
[2026-06-08T08:52:32] Filtering end-to-end fusions with low support (remaining=807)
[2026-06-08T08:52:33] Filtering fusions with no coverage around the breakpoints (remaining=792)
[2026-06-08T08:52:33] Indexing gene sequences 
[2026-06-08T08:52:38] Filtering genes with >=30% identity (remaining=260)
[2026-06-08T08:52:39] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=84)
[2026-06-08T08:52:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=78)
[2026-06-08T08:52:42] Searching for additional isoforms (remaining=95)
[2026-06-08T08:52:44] Assigning confidence scores to events 
[2026-06-08T08:52:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:52:47] Writing fusions to file 'aih-tih-sc-d666f1-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:52:48] Writing discarded fusions to file 'aih-tih-sc-d666f1-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:53:14] Freeing resources
[2026-06-08T08:53:34] Done (elapsed time=00:11:16, CPU time=00:11:15, peak memory=18.8gb)