[2026-06-08T08:49:22] Launching Arriba 2.4.0
[2026-06-08T08:49:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:34] Reading chimeric alignments from 'tih_rna_sample_00121_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=10245648)
[2026-06-08T08:56:34] Marking multi-mapping alignments (marked=6469172)
[2026-06-08T08:56:39] Detecting strandedness (reverse)
[2026-06-08T08:56:39] Assigning strands to alignments 
[2026-06-08T08:56:42] Annotating alignments 
[2026-06-08T08:57:23] Filtering duplicates (remaining=5497624)
[2026-06-08T08:57:32] 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=5215470)
[2026-06-08T08:57:35] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5215470)
[2026-06-08T08:57:38] Filtering viral contigs with expression lower than the top 5 (remaining=5215470)
[2026-06-08T08:57:45] Filtering viral contigs with less than 5% coverage (remaining=5215470)
[2026-06-08T08:57:49] Estimating fragment length (mate gap mean=-87.6446, mate gap stddev=28.9428, read length mean=133.23)
[2026-06-08T08:57:49] Filtering read-through fragments with a distance <=10000bp (remaining=4849770)
[2026-06-08T08:57:52] Filtering inconsistently clipped mates (remaining=4757468)
[2026-06-08T08:57:56] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4612501)
[2026-06-08T08:58:02] Filtering fragments with small insert size (remaining=4611663)
[2026-06-08T08:58:05] Filtering alignments with long gaps (remaining=4611662)
[2026-06-08T08:58:08] Filtering fragments with both mates in the same gene (remaining=4610655)
[2026-06-08T08:58:11] Filtering fusions arising from hairpin structures (remaining=4321514)
[2026-06-08T08:58:14] Filtering reads with a mismatch p-value <=0.01 (remaining=1915533)
[2026-06-08T08:58:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=912397)
[2026-06-08T08:58:38] Finding fusions and counting supporting reads (total=692822)
[2026-06-08T08:58:56] Merging adjacent fusion breakpoints (remaining=686880)
[2026-06-08T08:58:58] Filtering multi-mapping fusions by alignment score and read support (remaining=441024)
[2026-06-08T08:59:35] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:42] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=438320)
[2026-06-08T08:59:43] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=236613)
[2026-06-08T08:59:44] Filtering fusions with <2 supporting reads (remaining=35875)
[2026-06-08T08:59:45] Filtering fusions with an e-value >=0.3 (remaining=11252)
[2026-06-08T08:59:45] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11310)
[2026-06-08T08:59:49] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11228)
[2026-06-08T08:59:50] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11228)
[2026-06-08T08:59:52] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7606)
[2026-06-08T08:59:57] Searching for fusions with spliced split reads (remaining=7733)
[2026-06-08T09:00:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=4712)
[2026-06-08T09:00:04] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4649)
[2026-06-08T09:00:04] Searching for fusions with >=4 spliced events (remaining=5540)
[2026-06-08T09:00:06] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1897)
[2026-06-08T09:00:22] Filtering fusions with anchors <=23nt (remaining=1568)
[2026-06-08T09:00:23] Filtering end-to-end fusions with low support (remaining=1540)
[2026-06-08T09:00:24] Filtering fusions with no coverage around the breakpoints (remaining=1503)
[2026-06-08T09:00:24] Indexing gene sequences 
[2026-06-08T09:00:31] Filtering genes with >=30% identity (remaining=510)
[2026-06-08T09:00:34] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=262)
[2026-06-08T09:00:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=201)
[2026-06-08T09:00:39] Searching for additional isoforms (remaining=258)
[2026-06-08T09:00:40] Assigning confidence scores to events 
[2026-06-08T09:00:43] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:44] Writing fusions to file 'tih_rna_sample_00121_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T09:00:45] Writing discarded fusions to file 'tih_rna_sample_00121_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:19] Freeing resources
[2026-06-08T09:01:39] Done (elapsed time=00:12:17, CPU time=00:12:16, peak memory=15gb)