[2026-06-08T08:44:29] Launching Arriba 2.4.0
[2026-06-08T08:44:29] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:44:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:44:42] Reading chimeric alignments from 'aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11115020)
[2026-06-08T08:51:29] Marking multi-mapping alignments (marked=7576376)
[2026-06-08T08:51:33] Detecting strandedness (reverse)
[2026-06-08T08:51:33] Assigning strands to alignments 
[2026-06-08T08:51:35] Annotating alignments 
[2026-06-08T08:52:12] Filtering duplicates (remaining=6897245)
[2026-06-08T08:52:20] 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=6360130)
[2026-06-08T08:52:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6360130)
[2026-06-08T08:52:25] Filtering viral contigs with expression lower than the top 5 (remaining=6360130)
[2026-06-08T08:52:30] Filtering viral contigs with less than 5% coverage (remaining=6360130)
[2026-06-08T08:52:32] Estimating fragment length (mate gap mean=-86.6113, mate gap stddev=28.639, read length mean=126.174)
[2026-06-08T08:52:32] Filtering read-through fragments with a distance <=10000bp (remaining=6021583)
[2026-06-08T08:52:34] Filtering inconsistently clipped mates (remaining=5897769)
[2026-06-08T08:52:37] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5747347)
[2026-06-08T08:52:41] Filtering fragments with small insert size (remaining=5746272)
[2026-06-08T08:52:43] Filtering alignments with long gaps (remaining=5746272)
[2026-06-08T08:52:46] Filtering fragments with both mates in the same gene (remaining=5745172)
[2026-06-08T08:52:48] Filtering fusions arising from hairpin structures (remaining=5372746)
[2026-06-08T08:52:51] Filtering reads with a mismatch p-value <=0.01 (remaining=2091663)
[2026-06-08T08:53:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=959258)
[2026-06-08T08:53:15] Finding fusions and counting supporting reads (total=755938)
[2026-06-08T08:53:33] Merging adjacent fusion breakpoints (remaining=748590)
[2026-06-08T08:53:35] Filtering multi-mapping fusions by alignment score and read support (remaining=461805)
[2026-06-08T08:54:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:54:21] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=459846)
[2026-06-08T08:54:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=276980)
[2026-06-08T08:54:23] Filtering fusions with <2 supporting reads (remaining=32118)
[2026-06-08T08:54:24] Filtering fusions with an e-value >=0.3 (remaining=8911)
[2026-06-08T08:54:24] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8974)
[2026-06-08T08:54:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8905)
[2026-06-08T08:54:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8905)
[2026-06-08T08:54:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6195)
[2026-06-08T08:54:37] Searching for fusions with spliced split reads (remaining=6219)
[2026-06-08T08:54:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=4120)
[2026-06-08T08:54:43] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4059)
[2026-06-08T08:54:44] Searching for fusions with >=4 spliced events (remaining=4910)
[2026-06-08T08:54:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1998)
[2026-06-08T08:54:59] Filtering fusions with anchors <=23nt (remaining=1545)
[2026-06-08T08:55:00] Filtering end-to-end fusions with low support (remaining=1493)
[2026-06-08T08:55:01] Filtering fusions with no coverage around the breakpoints (remaining=1468)
[2026-06-08T08:55:02] Indexing gene sequences 
[2026-06-08T08:55:08] Filtering genes with >=30% identity (remaining=464)
[2026-06-08T08:55:11] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=246)
[2026-06-08T08:55:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=216)
[2026-06-08T08:55:20] Searching for additional isoforms (remaining=256)
[2026-06-08T08:55:21] Assigning confidence scores to events 
[2026-06-08T08:55:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:55:25] Writing fusions to file 'aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:55:26] Writing discarded fusions to file 'aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:56:00] Freeing resources
[2026-06-08T08:56:17] Done (elapsed time=00:11:48, CPU time=00:11:47, peak memory=16gb)