[2026-05-28T00:03:46] Launching Arriba 2.4.0
[2026-05-28T00:03:46] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:03:55] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:03:59] Reading chimeric alignments from '659_ezg-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3568432)
[2026-05-28T00:06:15] Marking multi-mapping alignments (marked=2283758)
[2026-05-28T00:06:16] Detecting strandedness (no)
[2026-05-28T00:06:16] Annotating alignments 
[2026-05-28T00:06:31] Filtering duplicates (remaining=1991864)
[2026-05-28T00:06:33] 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=1875701)
[2026-05-28T00:06:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1875701)
[2026-05-28T00:06:34] Filtering viral contigs with expression lower than the top 5 (remaining=1875701)
[2026-05-28T00:06:35] Filtering viral contigs with less than 5% coverage (remaining=1875701)
[2026-05-28T00:06:36] Estimating fragment length (mate gap mean=-88.9349, mate gap stddev=28.3291, read length mean=132.494)
[2026-05-28T00:06:36] Filtering read-through fragments with a distance <=10000bp (remaining=1729885)
[2026-05-28T00:06:37] Filtering inconsistently clipped mates (remaining=1701103)
[2026-05-28T00:06:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1653413)
[2026-05-28T00:06:39] Filtering fragments with small insert size (remaining=1653199)
[2026-05-28T00:06:40] Filtering alignments with long gaps (remaining=1653199)
[2026-05-28T00:06:41] Filtering fragments with both mates in the same gene (remaining=1652908)
[2026-05-28T00:06:41] Filtering fusions arising from hairpin structures (remaining=1557706)
[2026-05-28T00:06:42] Filtering reads with a mismatch p-value <=0.01 (remaining=704388)
[2026-05-28T00:06:47] Filtering reads with low entropy (k-mer content >=60%) (remaining=335138)
[2026-05-28T00:06:50] Finding fusions and counting supporting reads (total=287236)
[2026-05-28T00:06:55] Merging adjacent fusion breakpoints (remaining=284542)
[2026-05-28T00:06:56] Filtering multi-mapping fusions by alignment score and read support (remaining=175685)
[2026-05-28T00:07:08] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:07:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=174775)
[2026-05-28T00:07:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=88078)
[2026-05-28T00:07:11] Filtering fusions with <2 supporting reads (remaining=11183)
[2026-05-28T00:07:11] Filtering fusions with an e-value >=0.3 (remaining=3294)
[2026-05-28T00:07:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3337)
[2026-05-28T00:07:13] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3284)
[2026-05-28T00:07:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3285)
[2026-05-28T00:07:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2696)
[2026-05-28T00:07:15] Searching for fusions with spliced split reads (remaining=2835)
[2026-05-28T00:07:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=2079)
[2026-05-28T00:07:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2066)
[2026-05-28T00:07:17] Searching for fusions with >=4 spliced events (remaining=2281)
[2026-05-28T00:07:18] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=691)
[2026-05-28T00:07:29] Filtering fusions with anchors <=23nt (remaining=550)
[2026-05-28T00:07:29] Filtering end-to-end fusions with low support (remaining=536)
[2026-05-28T00:07:30] Filtering fusions with no coverage around the breakpoints (remaining=525)
[2026-05-28T00:07:30] Indexing gene sequences 
[2026-05-28T00:07:33] Filtering genes with >=30% identity (remaining=192)
[2026-05-28T00:07:34] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=99)
[2026-05-28T00:07:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=84)
[2026-05-28T00:07:35] Searching for additional isoforms (remaining=107)
[2026-05-28T00:07:35] Assigning confidence scores to events 
[2026-05-28T00:07:37] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:07:37] Writing fusions to file '659_ezg-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:07:37] Writing discarded fusions to file '659_ezg-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:07:48] Freeing resources
[2026-05-28T00:07:54] Done (elapsed time=00:04:08, CPU time=00:04:07, peak memory=7.93gb)