[2026-06-08T08:45:17] Launching Arriba 2.4.0
[2026-06-08T08:45:17] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:45:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:45:33] Reading chimeric alignments from 'tih_rna_sample_00586_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=7888179)
[2026-06-08T08:50:00] Marking multi-mapping alignments (marked=5162139)
[2026-06-08T08:50:02] Detecting strandedness (reverse)
[2026-06-08T08:50:02] Assigning strands to alignments 
[2026-06-08T08:50:04] Annotating alignments 
[2026-06-08T08:50:25] Filtering duplicates (remaining=5234103)
[2026-06-08T08:50:29] 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=4931755)
[2026-06-08T08:50:31] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4931755)
[2026-06-08T08:50:32] Filtering viral contigs with expression lower than the top 5 (remaining=4931755)
[2026-06-08T08:50:35] Filtering viral contigs with less than 5% coverage (remaining=4931755)
[2026-06-08T08:50:37] Estimating fragment length (mate gap mean=-86.2462, mate gap stddev=32.5035, read length mean=137.47)
[2026-06-08T08:50:37] Filtering read-through fragments with a distance <=10000bp (remaining=4657799)
[2026-06-08T08:50:38] Filtering inconsistently clipped mates (remaining=4596739)
[2026-06-08T08:50:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4501777)
[2026-06-08T08:50:43] Filtering fragments with small insert size (remaining=4501370)
[2026-06-08T08:50:44] Filtering alignments with long gaps (remaining=4501370)
[2026-06-08T08:50:45] Filtering fragments with both mates in the same gene (remaining=4500518)
[2026-06-08T08:50:47] Filtering fusions arising from hairpin structures (remaining=4242799)
[2026-06-08T08:50:48] Filtering reads with a mismatch p-value <=0.01 (remaining=2048554)
[2026-06-08T08:50:59] Filtering reads with low entropy (k-mer content >=60%) (remaining=670037)
[2026-06-08T08:51:07] Finding fusions and counting supporting reads (total=510863)
[2026-06-08T08:51:18] Merging adjacent fusion breakpoints (remaining=505495)
[2026-06-08T08:51:19] Filtering multi-mapping fusions by alignment score and read support (remaining=322848)
[2026-06-08T08:51:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:51:46] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=320620)
[2026-06-08T08:51:46] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=173572)
[2026-06-08T08:51:47] Filtering fusions with <2 supporting reads (remaining=23080)
[2026-06-08T08:51:48] Filtering fusions with an e-value >=0.3 (remaining=9173)
[2026-06-08T08:51:48] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9224)
[2026-06-08T08:51:51] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9161)
[2026-06-08T08:51:51] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9161)
[2026-06-08T08:51:52] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5766)
[2026-06-08T08:51:56] Searching for fusions with spliced split reads (remaining=5858)
[2026-06-08T08:51:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=3279)
[2026-06-08T08:52:00] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3223)
[2026-06-08T08:52:01] Searching for fusions with >=4 spliced events (remaining=3620)
[2026-06-08T08:52:02] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1232)
[2026-06-08T08:52:15] Filtering fusions with anchors <=23nt (remaining=877)
[2026-06-08T08:52:16] Filtering end-to-end fusions with low support (remaining=829)
[2026-06-08T08:52:16] Filtering fusions with no coverage around the breakpoints (remaining=803)
[2026-06-08T08:52:17] Indexing gene sequences 
[2026-06-08T08:52:21] Filtering genes with >=30% identity (remaining=252)
[2026-06-08T08:52:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=118)
[2026-06-08T08:52:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=115)
[2026-06-08T08:52:25] Searching for additional isoforms (remaining=149)
[2026-06-08T08:52:26] Assigning confidence scores to events 
[2026-06-08T08:52:28] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:52:29] Writing fusions to file 'tih_rna_sample_00586_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:52:30] Writing discarded fusions to file 'tih_rna_sample_00586_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:52:50] Freeing resources
[2026-06-08T08:53:02] Done (elapsed time=00:07:45, CPU time=00:07:43, peak memory=12.4gb)