[2026-06-08T08:43:22] Launching Arriba 2.4.0
[2026-06-08T08:43:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:43:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:43:40] Reading chimeric alignments from 'tih_rna_sample_00658_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=9406111)
[2026-06-08T08:50:39] Marking multi-mapping alignments (marked=5935373)
[2026-06-08T08:50:43] Detecting strandedness (reverse)
[2026-06-08T08:50:43] Assigning strands to alignments 
[2026-06-08T08:50:45] Annotating alignments 
[2026-06-08T08:51:16] Filtering duplicates (remaining=5842796)
[2026-06-08T08:51:22] 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=5551475)
[2026-06-08T08:51:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5551475)
[2026-06-08T08:51:26] Filtering viral contigs with expression lower than the top 5 (remaining=5551475)
[2026-06-08T08:51:30] Filtering viral contigs with less than 5% coverage (remaining=5551475)
[2026-06-08T08:51:32] Estimating fragment length (mate gap mean=-86.8592, mate gap stddev=28.1246, read length mean=130.621)
[2026-06-08T08:51:32] Filtering read-through fragments with a distance <=10000bp (remaining=5262795)
[2026-06-08T08:51:34] Filtering inconsistently clipped mates (remaining=5156587)
[2026-06-08T08:51:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5050828)
[2026-06-08T08:51:39] Filtering fragments with small insert size (remaining=5049813)
[2026-06-08T08:51:41] Filtering alignments with long gaps (remaining=5049813)
[2026-06-08T08:51:43] Filtering fragments with both mates in the same gene (remaining=5049030)
[2026-06-08T08:51:45] Filtering fusions arising from hairpin structures (remaining=4695811)
[2026-06-08T08:51:48] Filtering reads with a mismatch p-value <=0.01 (remaining=2278160)
[2026-06-08T08:52:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=845866)
[2026-06-08T08:52:17] Finding fusions and counting supporting reads (total=620426)
[2026-06-08T08:52:37] Merging adjacent fusion breakpoints (remaining=614619)
[2026-06-08T08:52:38] Filtering multi-mapping fusions by alignment score and read support (remaining=387494)
[2026-06-08T08:53:15] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:53:21] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=385888)
[2026-06-08T08:53:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=217214)
[2026-06-08T08:53:23] Filtering fusions with <2 supporting reads (remaining=29031)
[2026-06-08T08:53:23] Filtering fusions with an e-value >=0.3 (remaining=6826)
[2026-06-08T08:53:24] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6886)
[2026-06-08T08:53:27] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6824)
[2026-06-08T08:53:28] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6824)
[2026-06-08T08:53:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6548)
[2026-06-08T08:53:34] Searching for fusions with spliced split reads (remaining=6625)
[2026-06-08T08:53:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=4403)
[2026-06-08T08:53:39] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4346)
[2026-06-08T08:53:40] Searching for fusions with >=4 spliced events (remaining=5056)
[2026-06-08T08:53:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1694)
[2026-06-08T08:53:57] Filtering fusions with anchors <=23nt (remaining=1380)
[2026-06-08T08:53:58] Filtering end-to-end fusions with low support (remaining=1332)
[2026-06-08T08:53:59] Filtering fusions with no coverage around the breakpoints (remaining=1285)
[2026-06-08T08:53:59] Indexing gene sequences 
[2026-06-08T08:54:07] Filtering genes with >=30% identity (remaining=382)
[2026-06-08T08:54:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=197)
[2026-06-08T08:54:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=186)
[2026-06-08T08:54:23] Searching for additional isoforms (remaining=233)
[2026-06-08T08:54:24] Assigning confidence scores to events 
[2026-06-08T08:54:28] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:54:28] Writing fusions to file 'tih_rna_sample_00658_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:54:31] Writing discarded fusions to file 'tih_rna_sample_00658_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:55:06] Freeing resources
[2026-06-08T08:55:23] Done (elapsed time=00:12:01, CPU time=00:12:01, peak memory=14gb)