[2026-06-08T08:32:33] Launching Arriba 2.4.0
[2026-06-08T08:32:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:48] Reading chimeric alignments from 'tih_rna_sample_00737_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11484685)
[2026-06-08T08:39:20] Marking multi-mapping alignments (marked=7430360)
[2026-06-08T08:39:25] Detecting strandedness (reverse)
[2026-06-08T08:39:25] Assigning strands to alignments 
[2026-06-08T08:39:28] Annotating alignments 
[2026-06-08T08:40:03] Filtering duplicates (remaining=6966400)
[2026-06-08T08:40:11] 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=6645521)
[2026-06-08T08:40:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6645521)
[2026-06-08T08:40:15] Filtering viral contigs with expression lower than the top 5 (remaining=6645521)
[2026-06-08T08:40:20] Filtering viral contigs with less than 5% coverage (remaining=6645521)
[2026-06-08T08:40:22] Estimating fragment length (mate gap mean=-87.5382, mate gap stddev=28.247, read length mean=129.635)
[2026-06-08T08:40:22] Filtering read-through fragments with a distance <=10000bp (remaining=6200922)
[2026-06-08T08:40:24] Filtering inconsistently clipped mates (remaining=6088642)
[2026-06-08T08:40:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5959866)
[2026-06-08T08:40:31] Filtering fragments with small insert size (remaining=5959099)
[2026-06-08T08:40:33] Filtering alignments with long gaps (remaining=5959099)
[2026-06-08T08:40:35] Filtering fragments with both mates in the same gene (remaining=5958030)
[2026-06-08T08:40:37] Filtering fusions arising from hairpin structures (remaining=5590978)
[2026-06-08T08:40:39] Filtering reads with a mismatch p-value <=0.01 (remaining=2633709)
[2026-06-08T08:40:52] Filtering reads with low entropy (k-mer content >=60%) (remaining=1031854)
[2026-06-08T08:41:03] Finding fusions and counting supporting reads (total=796764)
[2026-06-08T08:41:20] Merging adjacent fusion breakpoints (remaining=788488)
[2026-06-08T08:41:22] Filtering multi-mapping fusions by alignment score and read support (remaining=471744)
[2026-06-08T08:41:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:42:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=469897)
[2026-06-08T08:42:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=274786)
[2026-06-08T08:42:02] Filtering fusions with <2 supporting reads (remaining=32251)
[2026-06-08T08:42:03] Filtering fusions with an e-value >=0.3 (remaining=8181)
[2026-06-08T08:42:04] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8242)
[2026-06-08T08:42:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8138)
[2026-06-08T08:42:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8139)
[2026-06-08T08:42:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7052)
[2026-06-08T08:42:15] Searching for fusions with spliced split reads (remaining=7071)
[2026-06-08T08:42:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=4457)
[2026-06-08T08:42:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4400)
[2026-06-08T08:42:22] Searching for fusions with >=4 spliced events (remaining=5547)
[2026-06-08T08:42:24] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2664)
[2026-06-08T08:42:42] Filtering fusions with anchors <=23nt (remaining=2222)
[2026-06-08T08:42:43] Filtering end-to-end fusions with low support (remaining=2159)
[2026-06-08T08:42:44] Filtering fusions with no coverage around the breakpoints (remaining=2119)
[2026-06-08T08:42:44] Indexing gene sequences 
[2026-06-08T08:42:52] Filtering genes with >=30% identity (remaining=669)
[2026-06-08T08:42:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=274)
[2026-06-08T08:43:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=207)
[2026-06-08T08:43:02] Searching for additional isoforms (remaining=310)
[2026-06-08T08:43:03] Assigning confidence scores to events 
[2026-06-08T08:43:07] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:43:07] Writing fusions to file 'tih_rna_sample_00737_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:43:09] Writing discarded fusions to file 'tih_rna_sample_00737_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:43:42] Freeing resources
[2026-06-08T08:44:00] Done (elapsed time=00:11:27, CPU time=00:11:26, peak memory=16.2gb)