[2026-06-08T07:45:15] Launching Arriba 2.4.0
[2026-06-08T07:45:15] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:45:28] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:45:33] Reading chimeric alignments from 'tih_rna_sample_00575_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=5375624)
[2026-06-08T07:48:00] Marking multi-mapping alignments (marked=3880816)
[2026-06-08T07:48:03] Detecting strandedness (reverse)
[2026-06-08T07:48:03] Assigning strands to alignments 
[2026-06-08T07:48:04] Annotating alignments 
[2026-06-08T07:48:35] Filtering duplicates (remaining=1816191)
[2026-06-08T07:48:41] 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=1606814)
[2026-06-08T07:48:42] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1606814)
[2026-06-08T07:48:44] Filtering viral contigs with expression lower than the top 5 (remaining=1606814)
[2026-06-08T07:48:47] Filtering viral contigs with less than 5% coverage (remaining=1606814)
[2026-06-08T07:48:49] Estimating fragment length (mate gap mean=-83.2325, mate gap stddev=27.7548, read length mean=115.035)
[2026-06-08T07:48:49] Filtering read-through fragments with a distance <=10000bp (remaining=1563164)
[2026-06-08T07:48:50] Filtering inconsistently clipped mates (remaining=1529262)
[2026-06-08T07:48:52] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1489130)
[2026-06-08T07:48:54] Filtering fragments with small insert size (remaining=1488571)
[2026-06-08T07:48:55] Filtering alignments with long gaps (remaining=1488571)
[2026-06-08T07:48:57] Filtering fragments with both mates in the same gene (remaining=1488207)
[2026-06-08T07:48:58] Filtering fusions arising from hairpin structures (remaining=1402974)
[2026-06-08T07:49:00] Filtering reads with a mismatch p-value <=0.01 (remaining=406860)
[2026-06-08T07:49:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=136891)
[2026-06-08T07:49:10] Finding fusions and counting supporting reads (total=127424)
[2026-06-08T07:49:21] Merging adjacent fusion breakpoints (remaining=125950)
[2026-06-08T07:49:21] Filtering multi-mapping fusions by alignment score and read support (remaining=72588)
[2026-06-08T07:49:49] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:49:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=72220)
[2026-06-08T07:49:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=46501)
[2026-06-08T07:49:53] Filtering fusions with <2 supporting reads (remaining=3327)
[2026-06-08T07:49:54] Filtering fusions with an e-value >=0.3 (remaining=684)
[2026-06-08T07:49:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=698)
[2026-06-08T07:49:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=675)
[2026-06-08T07:49:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=675)
[2026-06-08T07:49:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=635)
[2026-06-08T07:50:00] Searching for fusions with spliced split reads (remaining=666)
[2026-06-08T07:50:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=532)
[2026-06-08T07:50:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=525)
[2026-06-08T07:50:03] Searching for fusions with >=4 spliced events (remaining=534)
[2026-06-08T07:50:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=221)
[2026-06-08T07:50:21] Filtering fusions with anchors <=23nt (remaining=138)
[2026-06-08T07:50:22] Filtering end-to-end fusions with low support (remaining=112)
[2026-06-08T07:50:22] Filtering fusions with no coverage around the breakpoints (remaining=103)
[2026-06-08T07:50:22] Indexing gene sequences 
[2026-06-08T07:50:24] Filtering genes with >=30% identity (remaining=40)
[2026-06-08T07:50:25] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=30)
[2026-06-08T07:50:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=30)
[2026-06-08T07:50:26] Searching for additional isoforms (remaining=32)
[2026-06-08T07:50:26] Assigning confidence scores to events 
[2026-06-08T07:50:28] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:50:28] Writing fusions to file 'tih_rna_sample_00575_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T07:50:29] Writing discarded fusions to file 'tih_rna_sample_00575_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:50:46] Freeing resources
[2026-06-08T07:51:02] Done (elapsed time=00:05:47, CPU time=00:05:45, peak memory=9.68gb)