[2026-06-08T07:34:58] Launching Arriba 2.4.0
[2026-06-08T07:34:58] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:35:17] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:35:23] Reading chimeric alignments from 'tih_rna_sample_00584_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=2238723)
[2026-06-08T07:36:48] Marking multi-mapping alignments (marked=1637007)
[2026-06-08T07:36:49] Detecting strandedness (reverse)
[2026-06-08T07:36:49] Assigning strands to alignments 
[2026-06-08T07:36:49] Annotating alignments 
[2026-06-08T07:36:59] Filtering duplicates (remaining=794464)
[2026-06-08T07:37:01] 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=678003)
[2026-06-08T07:37:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=678003)
[2026-06-08T07:37:02] Filtering viral contigs with expression lower than the top 5 (remaining=678003)
[2026-06-08T07:37:02] Filtering viral contigs with less than 5% coverage (remaining=678003)
[2026-06-08T07:37:03] Estimating fragment length (mate gap mean=-80.3048, mate gap stddev=29.2382, read length mean=113.871)
[2026-06-08T07:37:03] Filtering read-through fragments with a distance <=10000bp (remaining=654803)
[2026-06-08T07:37:04] Filtering inconsistently clipped mates (remaining=638893)
[2026-06-08T07:37:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=621038)
[2026-06-08T07:37:05] Filtering fragments with small insert size (remaining=620801)
[2026-06-08T07:37:05] Filtering alignments with long gaps (remaining=620801)
[2026-06-08T07:37:06] Filtering fragments with both mates in the same gene (remaining=620618)
[2026-06-08T07:37:06] Filtering fusions arising from hairpin structures (remaining=582392)
[2026-06-08T07:37:07] Filtering reads with a mismatch p-value <=0.01 (remaining=203784)
[2026-06-08T07:37:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=60640)
[2026-06-08T07:37:10] Finding fusions and counting supporting reads (total=58329)
[2026-06-08T07:37:14] Merging adjacent fusion breakpoints (remaining=57828)
[2026-06-08T07:37:14] Filtering multi-mapping fusions by alignment score and read support (remaining=30688)
[2026-06-08T07:37:24] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:37:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=30422)
[2026-06-08T07:37:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=17791)
[2026-06-08T07:37:25] Filtering fusions with <2 supporting reads (remaining=1057)
[2026-06-08T07:37:25] Filtering fusions with an e-value >=0.3 (remaining=367)
[2026-06-08T07:37:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=383)
[2026-06-08T07:37:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=369)
[2026-06-08T07:37:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=369)
[2026-06-08T07:37:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=359)
[2026-06-08T07:37:27] Searching for fusions with spliced split reads (remaining=365)
[2026-06-08T07:37:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=296)
[2026-06-08T07:37:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=293)
[2026-06-08T07:37:28] Searching for fusions with >=4 spliced events (remaining=297)
[2026-06-08T07:37:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=107)
[2026-06-08T07:37:49] Filtering fusions with anchors <=23nt (remaining=82)
[2026-06-08T07:37:49] Filtering end-to-end fusions with low support (remaining=67)
[2026-06-08T07:37:49] Filtering fusions with no coverage around the breakpoints (remaining=58)
[2026-06-08T07:37:50] Indexing gene sequences 
[2026-06-08T07:37:51] Filtering genes with >=30% identity (remaining=29)
[2026-06-08T07:37:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=17)
[2026-06-08T07:37:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=17)
[2026-06-08T07:37:51] Searching for additional isoforms (remaining=17)
[2026-06-08T07:37:51] Assigning confidence scores to events 
[2026-06-08T07:37:52] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:37:52] Writing fusions to file 'tih_rna_sample_00584_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T07:37:52] Writing discarded fusions to file 'tih_rna_sample_00584_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:37:59] Freeing resources
[2026-06-08T07:38:04] Done (elapsed time=00:03:06, CPU time=00:03:05, peak memory=6.4gb)