[2026-06-08T08:47:36] Launching Arriba 2.4.0
[2026-06-08T08:47:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:48] Reading chimeric alignments from 'tih_rna_sample_00680_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10937827)
[2026-06-08T08:54:37] Marking multi-mapping alignments (marked=6803015)
[2026-06-08T08:54:42] Detecting strandedness (reverse)
[2026-06-08T08:54:42] Assigning strands to alignments 
[2026-06-08T08:54:45] Annotating alignments 
[2026-06-08T08:55:26] Filtering duplicates (remaining=7284102)
[2026-06-08T08:55:35] 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=6935597)
[2026-06-08T08:55:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6935597)
[2026-06-08T08:55:41] Filtering viral contigs with expression lower than the top 5 (remaining=6935597)
[2026-06-08T08:55:47] Filtering viral contigs with less than 5% coverage (remaining=6935597)
[2026-06-08T08:55:49] Estimating fragment length (mate gap mean=-88.3399, mate gap stddev=28.5982, read length mean=133.17)
[2026-06-08T08:55:50] Filtering read-through fragments with a distance <=10000bp (remaining=6513752)
[2026-06-08T08:55:52] Filtering inconsistently clipped mates (remaining=6400960)
[2026-06-08T08:55:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6269173)
[2026-06-08T08:56:01] Filtering fragments with small insert size (remaining=6268407)
[2026-06-08T08:56:03] Filtering alignments with long gaps (remaining=6268407)
[2026-06-08T08:56:06] Filtering fragments with both mates in the same gene (remaining=6267280)
[2026-06-08T08:56:09] Filtering fusions arising from hairpin structures (remaining=5890849)
[2026-06-08T08:56:12] Filtering reads with a mismatch p-value <=0.01 (remaining=2921282)
[2026-06-08T08:56:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=1092961)
[2026-06-08T08:56:41] Finding fusions and counting supporting reads (total=785806)
[2026-06-08T08:57:02] Merging adjacent fusion breakpoints (remaining=777096)
[2026-06-08T08:57:04] Filtering multi-mapping fusions by alignment score and read support (remaining=496834)
[2026-06-08T08:57:45] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=494806)
[2026-06-08T08:57:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=280454)
[2026-06-08T08:57:55] Filtering fusions with <2 supporting reads (remaining=38261)
[2026-06-08T08:57:56] Filtering fusions with an e-value >=0.3 (remaining=9953)
[2026-06-08T08:57:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10027)
[2026-06-08T08:58:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9931)
[2026-06-08T08:58:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9931)
[2026-06-08T08:58:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8324)
[2026-06-08T08:58:11] Searching for fusions with spliced split reads (remaining=8344)
[2026-06-08T08:58:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=5282)
[2026-06-08T08:58:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5189)
[2026-06-08T08:58:19] Searching for fusions with >=4 spliced events (remaining=6242)
[2026-06-08T08:58:21] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2353)
[2026-06-08T08:58:38] Filtering fusions with anchors <=23nt (remaining=1854)
[2026-06-08T08:58:39] Filtering end-to-end fusions with low support (remaining=1792)
[2026-06-08T08:58:40] Filtering fusions with no coverage around the breakpoints (remaining=1751)
[2026-06-08T08:58:41] Indexing gene sequences 
[2026-06-08T08:58:48] Filtering genes with >=30% identity (remaining=507)
[2026-06-08T08:58:52] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=236)
[2026-06-08T08:58:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=202)
[2026-06-08T08:59:00] Searching for additional isoforms (remaining=274)
[2026-06-08T08:59:02] Assigning confidence scores to events 
[2026-06-08T08:59:06] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:06] Writing fusions to file 'tih_rna_sample_00680_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:08] Writing discarded fusions to file 'tih_rna_sample_00680_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:47] Freeing resources
[2026-06-08T09:00:08] Done (elapsed time=00:12:32, CPU time=00:12:31, peak memory=15.6gb)