[2026-06-08T08:50:40] Launching Arriba 2.4.0
[2026-06-08T08:50:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:50:49] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:50:53] Reading chimeric alignments from 'tih_rna_sample_00594_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=12135967)
[2026-06-08T08:59:07] Marking multi-mapping alignments (marked=8082914)
[2026-06-08T08:59:13] Detecting strandedness (reverse)
[2026-06-08T08:59:13] Assigning strands to alignments 
[2026-06-08T08:59:16] Annotating alignments 
[2026-06-08T08:59:59] Filtering duplicates (remaining=7732296)
[2026-06-08T09:00:08] 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=7290776)
[2026-06-08T09:00:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7290776)
[2026-06-08T09:00:14] Filtering viral contigs with expression lower than the top 5 (remaining=7290776)
[2026-06-08T09:00:20] Filtering viral contigs with less than 5% coverage (remaining=7290776)
[2026-06-08T09:00:23] Estimating fragment length (mate gap mean=-86.9656, mate gap stddev=30.0446, read length mean=135.094)
[2026-06-08T09:00:23] Filtering read-through fragments with a distance <=10000bp (remaining=6823243)
[2026-06-08T09:00:25] Filtering inconsistently clipped mates (remaining=6723499)
[2026-06-08T09:00:28] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6578035)
[2026-06-08T09:00:34] Filtering fragments with small insert size (remaining=6577287)
[2026-06-08T09:00:36] Filtering alignments with long gaps (remaining=6577287)
[2026-06-08T09:00:39] Filtering fragments with both mates in the same gene (remaining=6576285)
[2026-06-08T09:00:42] Filtering fusions arising from hairpin structures (remaining=6173682)
[2026-06-08T09:00:45] Filtering reads with a mismatch p-value <=0.01 (remaining=3090412)
[2026-06-08T09:01:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=1045004)
[2026-06-08T09:01:19] Finding fusions and counting supporting reads (total=775801)
[2026-06-08T09:01:40] Merging adjacent fusion breakpoints (remaining=763534)
[2026-06-08T09:01:42] Filtering multi-mapping fusions by alignment score and read support (remaining=473470)
[2026-06-08T09:02:25] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:02:34] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=470162)
[2026-06-08T09:02:35] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=258909)
[2026-06-08T09:02:36] Filtering fusions with <2 supporting reads (remaining=34183)
[2026-06-08T09:02:37] Filtering fusions with an e-value >=0.3 (remaining=11527)
[2026-06-08T09:02:38] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11590)
[2026-06-08T09:02:43] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11483)
[2026-06-08T09:02:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11483)
[2026-06-08T09:02:45] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7841)
[2026-06-08T09:02:52] Searching for fusions with spliced split reads (remaining=7854)
[2026-06-08T09:02:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=4525)
[2026-06-08T09:03:00] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4481)
[2026-06-08T09:03:01] Searching for fusions with >=4 spliced events (remaining=5356)
[2026-06-08T09:03:02] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2144)
[2026-06-08T09:03:19] Filtering fusions with anchors <=23nt (remaining=1594)
[2026-06-08T09:03:20] Filtering end-to-end fusions with low support (remaining=1529)
[2026-06-08T09:03:21] Filtering fusions with no coverage around the breakpoints (remaining=1497)
[2026-06-08T09:03:22] Indexing gene sequences 
[2026-06-08T09:03:28] Filtering genes with >=30% identity (remaining=465)
[2026-06-08T09:03:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=192)
[2026-06-08T09:03:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=144)
[2026-06-08T09:03:37] Searching for additional isoforms (remaining=214)
[2026-06-08T09:03:38] Assigning confidence scores to events 
[2026-06-08T09:03:43] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:03:43] Writing fusions to file 'tih_rna_sample_00594_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:03:45] Writing discarded fusions to file 'tih_rna_sample_00594_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:04:21] Freeing resources
[2026-06-08T09:04:42] Done (elapsed time=00:14:02, CPU time=00:14:01, peak memory=16.7gb)