[2026-06-08T08:38:34] Launching Arriba 2.4.0
[2026-06-08T08:38:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:38:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:38:54] Reading chimeric alignments from 'tih_rna_sample_00457_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=10507896)
[2026-06-08T08:48:46] Marking multi-mapping alignments (marked=6659733)
[2026-06-08T08:48:53] Detecting strandedness (reverse)
[2026-06-08T08:48:53] Assigning strands to alignments 
[2026-06-08T08:48:57] Annotating alignments 
[2026-06-08T08:49:54] Filtering duplicates (remaining=5424306)
[2026-06-08T08:50:06] 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=5113138)
[2026-06-08T08:50:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5113138)
[2026-06-08T08:50:13] Filtering viral contigs with expression lower than the top 5 (remaining=5113138)
[2026-06-08T08:50:20] Filtering viral contigs with less than 5% coverage (remaining=5113138)
[2026-06-08T08:50:24] Estimating fragment length (mate gap mean=-88.1591, mate gap stddev=29.6058, read length mean=133.214)
[2026-06-08T08:50:24] Filtering read-through fragments with a distance <=10000bp (remaining=4781537)
[2026-06-08T08:50:28] Filtering inconsistently clipped mates (remaining=4709660)
[2026-06-08T08:50:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4588657)
[2026-06-08T08:50:38] Filtering fragments with small insert size (remaining=4587921)
[2026-06-08T08:50:41] Filtering alignments with long gaps (remaining=4587921)
[2026-06-08T08:50:45] Filtering fragments with both mates in the same gene (remaining=4587210)
[2026-06-08T08:50:48] Filtering fusions arising from hairpin structures (remaining=4364041)
[2026-06-08T08:50:52] Filtering reads with a mismatch p-value <=0.01 (remaining=1766933)
[2026-06-08T08:51:07] Filtering reads with low entropy (k-mer content >=60%) (remaining=795186)
[2026-06-08T08:51:19] Finding fusions and counting supporting reads (total=630269)
[2026-06-08T08:51:46] Merging adjacent fusion breakpoints (remaining=625170)
[2026-06-08T08:51:48] Filtering multi-mapping fusions by alignment score and read support (remaining=415093)
[2026-06-08T08:52:38] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:52:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=413271)
[2026-06-08T08:52:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=213093)
[2026-06-08T08:52:54] Filtering fusions with <2 supporting reads (remaining=30093)
[2026-06-08T08:52:55] Filtering fusions with an e-value >=0.3 (remaining=9666)
[2026-06-08T08:52:56] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9713)
[2026-06-08T08:53:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9652)
[2026-06-08T08:53:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9652)
[2026-06-08T08:53:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6181)
[2026-06-08T08:53:15] Searching for fusions with spliced split reads (remaining=6287)
[2026-06-08T08:53:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=4022)
[2026-06-08T08:53:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3964)
[2026-06-08T08:53:28] Searching for fusions with >=4 spliced events (remaining=4639)
[2026-06-08T08:53:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1737)
[2026-06-08T08:53:56] Filtering fusions with anchors <=23nt (remaining=1334)
[2026-06-08T08:53:57] Filtering end-to-end fusions with low support (remaining=1271)
[2026-06-08T08:53:58] Filtering fusions with no coverage around the breakpoints (remaining=1240)
[2026-06-08T08:53:59] Indexing gene sequences 
[2026-06-08T08:54:07] Filtering genes with >=30% identity (remaining=430)
[2026-06-08T08:54:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=225)
[2026-06-08T08:54:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=207)
[2026-06-08T08:54:18] Searching for additional isoforms (remaining=249)
[2026-06-08T08:54:20] Assigning confidence scores to events 
[2026-06-08T08:54:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:54:26] Writing fusions to file 'tih_rna_sample_00457_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:54:29] Writing discarded fusions to file 'tih_rna_sample_00457_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:55:23] Freeing resources
[2026-06-08T08:56:04] Done (elapsed time=00:17:30, CPU time=00:17:28, peak memory=15.2gb)