[2026-06-08T08:35:35] Launching Arriba 2.4.0
[2026-06-08T08:35:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:49] Reading chimeric alignments from 'tih_rna_sample_00654_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=13105334)
[2026-06-08T08:44:34] Marking multi-mapping alignments (marked=8340283)
[2026-06-08T08:44:43] Detecting strandedness (reverse)
[2026-06-08T08:44:43] Assigning strands to alignments 
[2026-06-08T08:44:48] Annotating alignments 
[2026-06-08T08:46:22] Filtering duplicates (remaining=8481694)
[2026-06-08T08:46:35] 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=7945509)
[2026-06-08T08:46:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7945509)
[2026-06-08T08:46:44] Filtering viral contigs with expression lower than the top 5 (remaining=7945509)
[2026-06-08T08:46:54] Filtering viral contigs with less than 5% coverage (remaining=7945509)
[2026-06-08T08:46:58] Estimating fragment length (mate gap mean=-88.0582, mate gap stddev=29.1884, read length mean=132.193)
[2026-06-08T08:46:58] Filtering read-through fragments with a distance <=10000bp (remaining=7507479)
[2026-06-08T08:47:03] Filtering inconsistently clipped mates (remaining=7416129)
[2026-06-08T08:47:07] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7288703)
[2026-06-08T08:47:16] Filtering fragments with small insert size (remaining=7287673)
[2026-06-08T08:47:21] Filtering alignments with long gaps (remaining=7287673)
[2026-06-08T08:47:26] Filtering fragments with both mates in the same gene (remaining=7286339)
[2026-06-08T08:47:32] Filtering fusions arising from hairpin structures (remaining=6948577)
[2026-06-08T08:47:38] Filtering reads with a mismatch p-value <=0.01 (remaining=3183025)
[2026-06-08T08:48:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=1294779)
[2026-06-08T08:48:27] Finding fusions and counting supporting reads (total=943549)
[2026-06-08T08:49:10] Merging adjacent fusion breakpoints (remaining=934756)
[2026-06-08T08:49:14] Filtering multi-mapping fusions by alignment score and read support (remaining=610508)
[2026-06-08T08:50:36] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:51:00] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=607374)
[2026-06-08T08:51:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=345711)
[2026-06-08T08:51:04] Filtering fusions with <2 supporting reads (remaining=49433)
[2026-06-08T08:51:06] Filtering fusions with an e-value >=0.3 (remaining=13987)
[2026-06-08T08:51:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14036)
[2026-06-08T08:51:16] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13936)
[2026-06-08T08:51:18] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13936)
[2026-06-08T08:51:22] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9520)
[2026-06-08T08:51:37] Searching for fusions with spliced split reads (remaining=9534)
[2026-06-08T08:51:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=5812)
[2026-06-08T08:51:55] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5745)
[2026-06-08T08:51:57] Searching for fusions with >=4 spliced events (remaining=7082)
[2026-06-08T08:52:00] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2841)
[2026-06-08T08:52:30] Filtering fusions with anchors <=23nt (remaining=2193)
[2026-06-08T08:52:32] Filtering end-to-end fusions with low support (remaining=2060)
[2026-06-08T08:52:34] Filtering fusions with no coverage around the breakpoints (remaining=2006)
[2026-06-08T08:52:36] Indexing gene sequences 
[2026-06-08T08:52:52] Filtering genes with >=30% identity (remaining=618)
[2026-06-08T08:53:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=283)
[2026-06-08T08:53:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=243)
[2026-06-08T08:53:12] Searching for additional isoforms (remaining=311)
[2026-06-08T08:53:15] Assigning confidence scores to events 
[2026-06-08T08:53:22] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:53:22] Writing fusions to file 'tih_rna_sample_00654_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:53:25] Writing discarded fusions to file 'tih_rna_sample_00654_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:54:43] Freeing resources
[2026-06-08T08:55:26] Done (elapsed time=00:19:51, CPU time=00:19:50, peak memory=18.1gb)