[2026-06-08T08:23:40] Launching Arriba 2.4.0
[2026-06-08T08:23:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:23:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:23:58] Reading chimeric alignments from 'tih_rna_sample_00090_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam' (total=16756461)
[2026-06-08T08:33:27] Marking multi-mapping alignments (marked=12279776)
[2026-06-08T08:33:35] Detecting strandedness (reverse)
[2026-06-08T08:33:35] Assigning strands to alignments 
[2026-06-08T08:33:39] Annotating alignments 
[2026-06-08T08:34:45] Filtering duplicates (remaining=9446718)
[2026-06-08T08:34:58] 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=8338525)
[2026-06-08T08:35:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8338525)
[2026-06-08T08:35:05] Filtering viral contigs with expression lower than the top 5 (remaining=8338525)
[2026-06-08T08:35:14] Filtering viral contigs with less than 5% coverage (remaining=8338525)
[2026-06-08T08:35:18] Estimating fragment length (mate gap mean=-80.9561, mate gap stddev=29.3699, read length mean=118.57)
[2026-06-08T08:35:18] Filtering read-through fragments with a distance <=10000bp (remaining=7757678)
[2026-06-08T08:35:22] Filtering inconsistently clipped mates (remaining=7558193)
[2026-06-08T08:35:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6754142)
[2026-06-08T08:35:34] Filtering fragments with small insert size (remaining=6749660)
[2026-06-08T08:35:38] Filtering alignments with long gaps (remaining=6749660)
[2026-06-08T08:35:42] Filtering fragments with both mates in the same gene (remaining=6748127)
[2026-06-08T08:35:47] Filtering fusions arising from hairpin structures (remaining=6201113)
[2026-06-08T08:35:52] Filtering reads with a mismatch p-value <=0.01 (remaining=2263891)
[2026-06-08T08:36:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=1503378)
[2026-06-08T08:36:27] Finding fusions and counting supporting reads (total=1317746)
[2026-06-08T08:37:01] Merging adjacent fusion breakpoints (remaining=1303939)
[2026-06-08T08:37:04] Filtering multi-mapping fusions by alignment score and read support (remaining=674495)
[2026-06-08T08:38:06] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:38:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=671302)
[2026-06-08T08:38:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=457605)
[2026-06-08T08:38:24] Filtering fusions with <2 supporting reads (remaining=29966)
[2026-06-08T08:38:25] Filtering fusions with an e-value >=0.3 (remaining=4957)
[2026-06-08T08:38:27] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5044)
[2026-06-08T08:38:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4832)
[2026-06-08T08:38:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4832)
[2026-06-08T08:38:38] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4709)
[2026-06-08T08:38:48] Searching for fusions with spliced split reads (remaining=4812)
[2026-06-08T08:38:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=3341)
[2026-06-08T08:39:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3320)
[2026-06-08T08:39:03] Searching for fusions with >=4 spliced events (remaining=4229)
[2026-06-08T08:39:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2004)
[2026-06-08T08:39:27] Filtering fusions with anchors <=23nt (remaining=1646)
[2026-06-08T08:39:28] Filtering end-to-end fusions with low support (remaining=1604)
[2026-06-08T08:39:30] Filtering fusions with no coverage around the breakpoints (remaining=1582)
[2026-06-08T08:39:31] Indexing gene sequences 
[2026-06-08T08:39:40] Filtering genes with >=30% identity (remaining=495)
[2026-06-08T08:39:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=152)
[2026-06-08T08:39:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=147)
[2026-06-08T08:39:49] Searching for additional isoforms (remaining=187)
[2026-06-08T08:39:52] Assigning confidence scores to events 
[2026-06-08T08:40:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:40:00] Writing fusions to file 'tih_rna_sample_00090_23H5VFLT4_s32.arriba.fusions.tsv' 
[2026-06-08T08:40:03] Writing discarded fusions to file 'tih_rna_sample_00090_23H5VFLT4_s32.arriba.fusions.discarded.tsv'
[2026-06-08T08:41:20] Freeing resources
[2026-06-08T08:41:56] Done (elapsed time=00:18:16, CPU time=00:18:15, peak memory=22.8gb)