[2026-06-08T08:32:06] Launching Arriba 2.4.0
[2026-06-08T08:32:06] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:19] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:23] Reading chimeric alignments from 'aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=8799147)
[2026-06-08T08:37:36] Marking multi-mapping alignments (marked=5857084)
[2026-06-08T08:37:40] Detecting strandedness (reverse)
[2026-06-08T08:37:40] Assigning strands to alignments 
[2026-06-08T08:37:41] Annotating alignments 
[2026-06-08T08:38:04] Filtering duplicates (remaining=4338458)
[2026-06-08T08:38:08] 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=4087089)
[2026-06-08T08:38:10] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4087089)
[2026-06-08T08:38:11] Filtering viral contigs with expression lower than the top 5 (remaining=4087089)
[2026-06-08T08:38:14] Filtering viral contigs with less than 5% coverage (remaining=4087089)
[2026-06-08T08:38:16] Estimating fragment length (mate gap mean=-87.5788, mate gap stddev=27.7474, read length mean=129.733)
[2026-06-08T08:38:16] Filtering read-through fragments with a distance <=10000bp (remaining=3907435)
[2026-06-08T08:38:17] Filtering inconsistently clipped mates (remaining=3845485)
[2026-06-08T08:38:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3719820)
[2026-06-08T08:38:21] Filtering fragments with small insert size (remaining=3719408)
[2026-06-08T08:38:22] Filtering alignments with long gaps (remaining=3719408)
[2026-06-08T08:38:24] Filtering fragments with both mates in the same gene (remaining=3718507)
[2026-06-08T08:38:25] Filtering fusions arising from hairpin structures (remaining=3562600)
[2026-06-08T08:38:27] Filtering reads with a mismatch p-value <=0.01 (remaining=1601654)
[2026-06-08T08:38:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=456664)
[2026-06-08T08:38:43] Finding fusions and counting supporting reads (total=361110)
[2026-06-08T08:38:55] Merging adjacent fusion breakpoints (remaining=357453)
[2026-06-08T08:38:56] Filtering multi-mapping fusions by alignment score and read support (remaining=204508)
[2026-06-08T08:39:22] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:39:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=203227)
[2026-06-08T08:39:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=125705)
[2026-06-08T08:39:27] Filtering fusions with <2 supporting reads (remaining=13920)
[2026-06-08T08:39:28] Filtering fusions with an e-value >=0.3 (remaining=3822)
[2026-06-08T08:39:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3862)
[2026-06-08T08:39:31] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3781)
[2026-06-08T08:39:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3781)
[2026-06-08T08:39:32] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3525)
[2026-06-08T08:39:35] Searching for fusions with spliced split reads (remaining=3594)
[2026-06-08T08:39:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=2560)
[2026-06-08T08:39:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2515)
[2026-06-08T08:39:40] Searching for fusions with >=4 spliced events (remaining=2831)
[2026-06-08T08:39:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=981)
[2026-06-08T08:39:55] Filtering fusions with anchors <=23nt (remaining=820)
[2026-06-08T08:39:55] Filtering end-to-end fusions with low support (remaining=805)
[2026-06-08T08:39:56] Filtering fusions with no coverage around the breakpoints (remaining=791)
[2026-06-08T08:39:56] Indexing gene sequences 
[2026-06-08T08:40:00] Filtering genes with >=30% identity (remaining=256)
[2026-06-08T08:40:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=144)
[2026-06-08T08:40:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=144)
[2026-06-08T08:40:05] Searching for additional isoforms (remaining=162)
[2026-06-08T08:40:05] Assigning confidence scores to events 
[2026-06-08T08:40:07] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:40:08] Writing fusions to file 'aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:40:09] Writing discarded fusions to file 'aih-tih-sc-d2f1f4-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:40:28] Freeing resources
[2026-06-08T08:40:41] Done (elapsed time=00:08:35, CPU time=00:08:35, peak memory=13.1gb)