[2026-06-08T08:28:36] Launching Arriba 2.4.0
[2026-06-08T08:28:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:28:49] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:28:52] Reading chimeric alignments from 'tih_rna_sample_00124_23H5VFLT4_s31.Aligned.sortedByCoord.out.bam' (total=10581099)
[2026-06-08T08:36:06] Marking multi-mapping alignments (marked=6640332)
[2026-06-08T08:36:11] Detecting strandedness (reverse)
[2026-06-08T08:36:11] Assigning strands to alignments 
[2026-06-08T08:36:13] Annotating alignments 
[2026-06-08T08:36:48] Filtering duplicates (remaining=6904021)
[2026-06-08T08:36:56] 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=6492524)
[2026-06-08T08:36:58] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6492524)
[2026-06-08T08:37:00] Filtering viral contigs with expression lower than the top 5 (remaining=6492524)
[2026-06-08T08:37:04] Filtering viral contigs with less than 5% coverage (remaining=6492524)
[2026-06-08T08:37:07] Estimating fragment length (mate gap mean=-87.5836, mate gap stddev=29.7513, read length mean=130.629)
[2026-06-08T08:37:07] Filtering read-through fragments with a distance <=10000bp (remaining=6003379)
[2026-06-08T08:37:09] Filtering inconsistently clipped mates (remaining=5874751)
[2026-06-08T08:37:11] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5467364)
[2026-06-08T08:37:17] Filtering fragments with small insert size (remaining=5465788)
[2026-06-08T08:37:19] Filtering alignments with long gaps (remaining=5465788)
[2026-06-08T08:37:21] Filtering fragments with both mates in the same gene (remaining=5464255)
[2026-06-08T08:37:24] Filtering fusions arising from hairpin structures (remaining=5000039)
[2026-06-08T08:37:26] Filtering reads with a mismatch p-value <=0.01 (remaining=2141618)
[2026-06-08T08:37:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=1422302)
[2026-06-08T08:37:51] Finding fusions and counting supporting reads (total=1131725)
[2026-06-08T08:38:09] Merging adjacent fusion breakpoints (remaining=1123088)
[2026-06-08T08:38:11] Filtering multi-mapping fusions by alignment score and read support (remaining=675316)
[2026-06-08T08:38:43] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:38:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=672713)
[2026-06-08T08:38:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=426958)
[2026-06-08T08:38:52] Filtering fusions with <2 supporting reads (remaining=42942)
[2026-06-08T08:38:53] Filtering fusions with an e-value >=0.3 (remaining=9760)
[2026-06-08T08:38:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9828)
[2026-06-08T08:38:57] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9650)
[2026-06-08T08:38:58] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9650)
[2026-06-08T08:39:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8185)
[2026-06-08T08:39:05] Searching for fusions with spliced split reads (remaining=8221)
[2026-06-08T08:39:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=5097)
[2026-06-08T08:39:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5007)
[2026-06-08T08:39:13] Searching for fusions with >=4 spliced events (remaining=5963)
[2026-06-08T08:39:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2061)
[2026-06-08T08:39:31] Filtering fusions with anchors <=23nt (remaining=1594)
[2026-06-08T08:39:32] Filtering end-to-end fusions with low support (remaining=1547)
[2026-06-08T08:39:33] Filtering fusions with no coverage around the breakpoints (remaining=1521)
[2026-06-08T08:39:33] Indexing gene sequences 
[2026-06-08T08:39:39] Filtering genes with >=30% identity (remaining=445)
[2026-06-08T08:39:42] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=204)
[2026-06-08T08:39:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=195)
[2026-06-08T08:39:48] Searching for additional isoforms (remaining=270)
[2026-06-08T08:39:50] Assigning confidence scores to events 
[2026-06-08T08:39:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:39:54] Writing fusions to file 'tih_rna_sample_00124_23H5VFLT4_s31.arriba.fusions.tsv' 
[2026-06-08T08:39:56] Writing discarded fusions to file 'tih_rna_sample_00124_23H5VFLT4_s31.arriba.fusions.discarded.tsv'
[2026-06-08T08:40:31] Freeing resources
[2026-06-08T08:40:49] Done (elapsed time=00:12:13, CPU time=00:12:12, peak memory=16gb)