[2026-06-08T07:40:57] Launching Arriba 2.4.0
[2026-06-08T07:40:57] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:41:15] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:41:22] Reading chimeric alignments from 'tih_rna_sample_00679_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=3462192)
[2026-06-08T07:43:46] Marking multi-mapping alignments (marked=2497965)
[2026-06-08T07:43:48] Detecting strandedness (reverse)
[2026-06-08T07:43:48] Assigning strands to alignments 
[2026-06-08T07:43:49] Annotating alignments 
[2026-06-08T07:44:06] Filtering duplicates (remaining=1289740)
[2026-06-08T07:44:09] 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=1166339)
[2026-06-08T07:44:10] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1166339)
[2026-06-08T07:44:11] Filtering viral contigs with expression lower than the top 5 (remaining=1166339)
[2026-06-08T07:44:12] Filtering viral contigs with less than 5% coverage (remaining=1166339)
[2026-06-08T07:44:13] Estimating fragment length (mate gap mean=-75.4992, mate gap stddev=26.7726, read length mean=108.111)
[2026-06-08T07:44:14] Filtering read-through fragments with a distance <=10000bp (remaining=1115311)
[2026-06-08T07:44:14] Filtering inconsistently clipped mates (remaining=1087325)
[2026-06-08T07:44:15] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1054523)
[2026-06-08T07:44:17] Filtering fragments with small insert size (remaining=1054104)
[2026-06-08T07:44:17] Filtering alignments with long gaps (remaining=1054104)
[2026-06-08T07:44:18] Filtering fragments with both mates in the same gene (remaining=1053852)
[2026-06-08T07:44:19] Filtering fusions arising from hairpin structures (remaining=988308)
[2026-06-08T07:44:20] Filtering reads with a mismatch p-value <=0.01 (remaining=330800)
[2026-06-08T07:44:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=124154)
[2026-06-08T07:44:26] Finding fusions and counting supporting reads (total=120290)
[2026-06-08T07:44:33] Merging adjacent fusion breakpoints (remaining=118840)
[2026-06-08T07:44:34] Filtering multi-mapping fusions by alignment score and read support (remaining=61151)
[2026-06-08T07:44:51] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:44:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=60813)
[2026-06-08T07:44:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=38600)
[2026-06-08T07:44:54] Filtering fusions with <2 supporting reads (remaining=2451)
[2026-06-08T07:44:54] Filtering fusions with an e-value >=0.3 (remaining=720)
[2026-06-08T07:44:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=746)
[2026-06-08T07:44:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=718)
[2026-06-08T07:44:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=718)
[2026-06-08T07:44:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=708)
[2026-06-08T07:44:58] Searching for fusions with spliced split reads (remaining=728)
[2026-06-08T07:45:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=584)
[2026-06-08T07:45:00] Filtering read-through fusions with breakpoints near the gene boundary (remaining=580)
[2026-06-08T07:45:00] Searching for fusions with >=4 spliced events (remaining=591)
[2026-06-08T07:45:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=230)
[2026-06-08T07:45:27] Filtering fusions with anchors <=23nt (remaining=177)
[2026-06-08T07:45:27] Filtering end-to-end fusions with low support (remaining=160)
[2026-06-08T07:45:27] Filtering fusions with no coverage around the breakpoints (remaining=153)
[2026-06-08T07:45:27] Indexing gene sequences 
[2026-06-08T07:45:29] Filtering genes with >=30% identity (remaining=59)
[2026-06-08T07:45:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=23)
[2026-06-08T07:45:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=23)
[2026-06-08T07:45:30] Searching for additional isoforms (remaining=23)
[2026-06-08T07:45:31] Assigning confidence scores to events 
[2026-06-08T07:45:32] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:45:32] Writing fusions to file 'tih_rna_sample_00679_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T07:45:32] Writing discarded fusions to file 'tih_rna_sample_00679_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:45:44] Freeing resources
[2026-06-08T07:45:52] Done (elapsed time=00:04:55, CPU time=00:04:54, peak memory=7.66gb)