[2026-06-08T08:19:39] Launching Arriba 2.4.0
[2026-06-08T08:19:39] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:19:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:19:52] Reading chimeric alignments from 'tih_rna_sample_00414_23H5VFLT4_s40.Aligned.sortedByCoord.out.bam' (total=10888232)
[2026-06-08T08:26:54] Marking multi-mapping alignments (marked=7235779)
[2026-06-08T08:26:58] Detecting strandedness (reverse)
[2026-06-08T08:26:58] Assigning strands to alignments 
[2026-06-08T08:27:01] Annotating alignments 
[2026-06-08T08:27:40] Filtering duplicates (remaining=7042506)
[2026-06-08T08:27:48] 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=6480848)
[2026-06-08T08:27:50] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6480848)
[2026-06-08T08:27:52] Filtering viral contigs with expression lower than the top 5 (remaining=6480848)
[2026-06-08T08:27:57] Filtering viral contigs with less than 5% coverage (remaining=6480848)
[2026-06-08T08:28:00] Estimating fragment length (mate gap mean=-85.2059, mate gap stddev=30.2947, read length mean=129.369)
[2026-06-08T08:28:00] Filtering read-through fragments with a distance <=10000bp (remaining=6044392)
[2026-06-08T08:28:02] Filtering inconsistently clipped mates (remaining=5905181)
[2026-06-08T08:28:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5467517)
[2026-06-08T08:28:09] Filtering fragments with small insert size (remaining=5466040)
[2026-06-08T08:28:12] Filtering alignments with long gaps (remaining=5466040)
[2026-06-08T08:28:14] Filtering fragments with both mates in the same gene (remaining=5464333)
[2026-06-08T08:28:16] Filtering fusions arising from hairpin structures (remaining=4999975)
[2026-06-08T08:28:19] Filtering reads with a mismatch p-value <=0.01 (remaining=2194256)
[2026-06-08T08:28:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=1357527)
[2026-06-08T08:28:44] Finding fusions and counting supporting reads (total=1147482)
[2026-06-08T08:29:03] Merging adjacent fusion breakpoints (remaining=1140264)
[2026-06-08T08:29:05] Filtering multi-mapping fusions by alignment score and read support (remaining=654881)
[2026-06-08T08:29:42] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:29:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=651745)
[2026-06-08T08:29:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=431950)
[2026-06-08T08:29:52] Filtering fusions with <2 supporting reads (remaining=33932)
[2026-06-08T08:29:53] Filtering fusions with an e-value >=0.3 (remaining=8693)
[2026-06-08T08:29:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8758)
[2026-06-08T08:29:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8501)
[2026-06-08T08:29:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8501)
[2026-06-08T08:30:01] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6611)
[2026-06-08T08:30:07] Searching for fusions with spliced split reads (remaining=6721)
[2026-06-08T08:30:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=3962)
[2026-06-08T08:30:14] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3896)
[2026-06-08T08:30:15] Searching for fusions with >=4 spliced events (remaining=4767)
[2026-06-08T08:30:17] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1891)
[2026-06-08T08:30:32] Filtering fusions with anchors <=23nt (remaining=1476)
[2026-06-08T08:30:33] Filtering end-to-end fusions with low support (remaining=1440)
[2026-06-08T08:30:34] Filtering fusions with no coverage around the breakpoints (remaining=1416)
[2026-06-08T08:30:35] Indexing gene sequences 
[2026-06-08T08:30:41] Filtering genes with >=30% identity (remaining=445)
[2026-06-08T08:30:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=197)
[2026-06-08T08:30:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=160)
[2026-06-08T08:30:49] Searching for additional isoforms (remaining=226)
[2026-06-08T08:30:50] Assigning confidence scores to events 
[2026-06-08T08:30:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:30:55] Writing fusions to file 'tih_rna_sample_00414_23H5VFLT4_s40.arriba.fusions.tsv' 
[2026-06-08T08:30:56] Writing discarded fusions to file 'tih_rna_sample_00414_23H5VFLT4_s40.arriba.fusions.discarded.tsv'
[2026-06-08T08:31:32] Freeing resources
[2026-06-08T08:31:51] Done (elapsed time=00:12:12, CPU time=00:12:12, peak memory=16.2gb)