[2026-06-08T08:52:36] Launching Arriba 2.4.0
[2026-06-08T08:52:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:51] Reading chimeric alignments from 'tih_rna_sample_00628_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11177380)
[2026-06-08T08:59:35] Marking multi-mapping alignments (marked=6678641)
[2026-06-08T08:59:40] Detecting strandedness (reverse)
[2026-06-08T08:59:40] Assigning strands to alignments 
[2026-06-08T08:59:42] Annotating alignments 
[2026-06-08T09:00:13] Filtering duplicates (remaining=7566396)
[2026-06-08T09:00:20] 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=7268965)
[2026-06-08T09:00:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7268965)
[2026-06-08T09:00:24] Filtering viral contigs with expression lower than the top 5 (remaining=7268965)
[2026-06-08T09:00:28] Filtering viral contigs with less than 5% coverage (remaining=7268965)
[2026-06-08T09:00:31] Estimating fragment length (mate gap mean=-84.5085, mate gap stddev=31.9679, read length mean=136.224)
[2026-06-08T09:00:31] Filtering read-through fragments with a distance <=10000bp (remaining=6873160)
[2026-06-08T09:00:33] Filtering inconsistently clipped mates (remaining=6787802)
[2026-06-08T09:00:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6640275)
[2026-06-08T09:00:39] Filtering fragments with small insert size (remaining=6639479)
[2026-06-08T09:00:41] Filtering alignments with long gaps (remaining=6639479)
[2026-06-08T09:00:43] Filtering fragments with both mates in the same gene (remaining=6638167)
[2026-06-08T09:00:45] Filtering fusions arising from hairpin structures (remaining=6299258)
[2026-06-08T09:00:47] Filtering reads with a mismatch p-value <=0.01 (remaining=3245556)
[2026-06-08T09:01:02] Filtering reads with low entropy (k-mer content >=60%) (remaining=1111144)
[2026-06-08T09:01:14] Finding fusions and counting supporting reads (total=817264)
[2026-06-08T09:01:30] Merging adjacent fusion breakpoints (remaining=809868)
[2026-06-08T09:01:32] Filtering multi-mapping fusions by alignment score and read support (remaining=553759)
[2026-06-08T09:02:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:02:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=550350)
[2026-06-08T09:02:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=296199)
[2026-06-08T09:02:11] Filtering fusions with <2 supporting reads (remaining=49093)
[2026-06-08T09:02:12] Filtering fusions with an e-value >=0.3 (remaining=20653)
[2026-06-08T09:02:12] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=20722)
[2026-06-08T09:02:16] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=20618)
[2026-06-08T09:02:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=20618)
[2026-06-08T09:02:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10151)
[2026-06-08T09:02:23] Searching for fusions with spliced split reads (remaining=10185)
[2026-06-08T09:02:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=4982)
[2026-06-08T09:02:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4917)
[2026-06-08T09:02:31] Searching for fusions with >=4 spliced events (remaining=5987)
[2026-06-08T09:02:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2135)
[2026-06-08T09:02:47] Filtering fusions with anchors <=23nt (remaining=1685)
[2026-06-08T09:02:48] Filtering end-to-end fusions with low support (remaining=1633)
[2026-06-08T09:02:49] Filtering fusions with no coverage around the breakpoints (remaining=1584)
[2026-06-08T09:02:49] Indexing gene sequences 
[2026-06-08T09:02:55] Filtering genes with >=30% identity (remaining=420)
[2026-06-08T09:02:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=190)
[2026-06-08T09:03:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=184)
[2026-06-08T09:03:05] Searching for additional isoforms (remaining=242)
[2026-06-08T09:03:06] Assigning confidence scores to events 
[2026-06-08T09:03:10] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:03:10] Writing fusions to file 'tih_rna_sample_00628_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:03:12] Writing discarded fusions to file 'tih_rna_sample_00628_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:03:41] Freeing resources
[2026-06-08T09:03:58] Done (elapsed time=00:11:22, CPU time=00:11:22, peak memory=15.8gb)