[2026-06-08T09:28:34] Launching Arriba 2.4.0
[2026-06-08T09:28:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:28:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:28:46] Reading chimeric alignments from 'tih_rna_sample_00616_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10186442)
[2026-06-08T09:35:27] Marking multi-mapping alignments (marked=5976653)
[2026-06-08T09:35:31] Detecting strandedness (reverse)
[2026-06-08T09:35:31] Assigning strands to alignments 
[2026-06-08T09:35:33] Annotating alignments 
[2026-06-08T09:36:04] Filtering duplicates (remaining=6860918)
[2026-06-08T09:36:11] 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=6621836)
[2026-06-08T09:36:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6621836)
[2026-06-08T09:36:15] Filtering viral contigs with expression lower than the top 5 (remaining=6621836)
[2026-06-08T09:36:19] Filtering viral contigs with less than 5% coverage (remaining=6621836)
[2026-06-08T09:36:22] Estimating fragment length (mate gap mean=-87.0587, mate gap stddev=28.8041, read length mean=133.8)
[2026-06-08T09:36:22] Filtering read-through fragments with a distance <=10000bp (remaining=6136550)
[2026-06-08T09:36:24] Filtering inconsistently clipped mates (remaining=6039424)
[2026-06-08T09:36:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5923552)
[2026-06-08T09:36:30] Filtering fragments with small insert size (remaining=5922625)
[2026-06-08T09:36:32] Filtering alignments with long gaps (remaining=5922624)
[2026-06-08T09:36:34] Filtering fragments with both mates in the same gene (remaining=5921566)
[2026-06-08T09:36:36] Filtering fusions arising from hairpin structures (remaining=5571224)
[2026-06-08T09:36:39] Filtering reads with a mismatch p-value <=0.01 (remaining=2887030)
[2026-06-08T09:36:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=1164727)
[2026-06-08T09:37:02] Finding fusions and counting supporting reads (total=817857)
[2026-06-08T09:37:17] Merging adjacent fusion breakpoints (remaining=809683)
[2026-06-08T09:37:19] Filtering multi-mapping fusions by alignment score and read support (remaining=552990)
[2026-06-08T09:37:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:37:55] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=550258)
[2026-06-08T09:37:56] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=279686)
[2026-06-08T09:37:57] Filtering fusions with <2 supporting reads (remaining=43209)
[2026-06-08T09:37:58] Filtering fusions with an e-value >=0.3 (remaining=12031)
[2026-06-08T09:37:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12091)
[2026-06-08T09:38:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11999)
[2026-06-08T09:38:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11999)
[2026-06-08T09:38:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9839)
[2026-06-08T09:38:10] Searching for fusions with spliced split reads (remaining=9857)
[2026-06-08T09:38:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=5616)
[2026-06-08T09:38:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5559)
[2026-06-08T09:38:17] Searching for fusions with >=4 spliced events (remaining=6662)
[2026-06-08T09:38:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2203)
[2026-06-08T09:38:33] Filtering fusions with anchors <=23nt (remaining=1786)
[2026-06-08T09:38:34] Filtering end-to-end fusions with low support (remaining=1742)
[2026-06-08T09:38:35] Filtering fusions with no coverage around the breakpoints (remaining=1710)
[2026-06-08T09:38:35] Indexing gene sequences 
[2026-06-08T09:38:41] Filtering genes with >=30% identity (remaining=498)
[2026-06-08T09:38:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=227)
[2026-06-08T09:38:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=211)
[2026-06-08T09:38:56] Searching for additional isoforms (remaining=259)
[2026-06-08T09:38:57] Assigning confidence scores to events 
[2026-06-08T09:39:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:39:01] Writing fusions to file 'tih_rna_sample_00616_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:39:03] Writing discarded fusions to file 'tih_rna_sample_00616_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:39:31] Freeing resources
[2026-06-08T09:39:48] Done (elapsed time=00:11:14, CPU time=00:11:13, peak memory=14.8gb)