[2026-06-08T08:35:18] Launching Arriba 2.4.0
[2026-06-08T08:35:18] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:28] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:33] Reading chimeric alignments from 'tih_rna_sample_00464_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9519162)
[2026-06-08T08:42:22] Marking multi-mapping alignments (marked=5952457)
[2026-06-08T08:42:28] Detecting strandedness (reverse)
[2026-06-08T08:42:28] Assigning strands to alignments 
[2026-06-08T08:42:31] Annotating alignments 
[2026-06-08T08:43:19] Filtering duplicates (remaining=3647530)
[2026-06-08T08:43:27] 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=3498181)
[2026-06-08T08:43:30] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3498181)
[2026-06-08T08:43:33] Filtering viral contigs with expression lower than the top 5 (remaining=3498181)
[2026-06-08T08:43:39] Filtering viral contigs with less than 5% coverage (remaining=3498181)
[2026-06-08T08:43:43] Estimating fragment length (mate gap mean=-87.7254, mate gap stddev=27.3155, read length mean=130.193)
[2026-06-08T08:43:43] Filtering read-through fragments with a distance <=10000bp (remaining=3282763)
[2026-06-08T08:43:46] Filtering inconsistently clipped mates (remaining=3231071)
[2026-06-08T08:43:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3109129)
[2026-06-08T08:43:54] Filtering fragments with small insert size (remaining=3108374)
[2026-06-08T08:43:57] Filtering alignments with long gaps (remaining=3108374)
[2026-06-08T08:44:00] Filtering fragments with both mates in the same gene (remaining=3107771)
[2026-06-08T08:44:03] Filtering fusions arising from hairpin structures (remaining=2970612)
[2026-06-08T08:44:06] Filtering reads with a mismatch p-value <=0.01 (remaining=1214582)
[2026-06-08T08:44:16] Filtering reads with low entropy (k-mer content >=60%) (remaining=544580)
[2026-06-08T08:44:25] Finding fusions and counting supporting reads (total=453796)
[2026-06-08T08:44:47] Merging adjacent fusion breakpoints (remaining=450706)
[2026-06-08T08:44:48] Filtering multi-mapping fusions by alignment score and read support (remaining=264535)
[2026-06-08T08:45:32] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:45:39] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=263061)
[2026-06-08T08:45:40] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=144191)
[2026-06-08T08:45:41] Filtering fusions with <2 supporting reads (remaining=17476)
[2026-06-08T08:45:42] Filtering fusions with an e-value >=0.3 (remaining=4637)
[2026-06-08T08:45:42] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4671)
[2026-06-08T08:45:47] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4611)
[2026-06-08T08:45:48] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4611)
[2026-06-08T08:45:49] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4022)
[2026-06-08T08:45:55] Searching for fusions with spliced split reads (remaining=4091)
[2026-06-08T08:46:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=2879)
[2026-06-08T08:46:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2838)
[2026-06-08T08:46:03] Searching for fusions with >=4 spliced events (remaining=3241)
[2026-06-08T08:46:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1189)
[2026-06-08T08:46:21] Filtering fusions with anchors <=23nt (remaining=1008)
[2026-06-08T08:46:22] Filtering end-to-end fusions with low support (remaining=972)
[2026-06-08T08:46:22] Filtering fusions with no coverage around the breakpoints (remaining=935)
[2026-06-08T08:46:23] Indexing gene sequences 
[2026-06-08T08:46:29] Filtering genes with >=30% identity (remaining=282)
[2026-06-08T08:46:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=123)
[2026-06-08T08:46:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=115)
[2026-06-08T08:46:33] Searching for additional isoforms (remaining=134)
[2026-06-08T08:46:35] Assigning confidence scores to events 
[2026-06-08T08:46:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:46:38] Writing fusions to file 'tih_rna_sample_00464_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:46:39] Writing discarded fusions to file 'tih_rna_sample_00464_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:12] Freeing resources
[2026-06-08T08:47:37] Done (elapsed time=00:12:19, CPU time=00:12:17, peak memory=13.9gb)