[2026-05-27T23:55:58] Launching Arriba 2.4.0
[2026-05-27T23:55:58] Loading assembly from 'ref_genome.fa' 
[2026-05-27T23:56:07] Loading annotation from 'ref_annot.gtf' 
[2026-05-27T23:56:10] Reading chimeric alignments from '659_bGc-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3628181)
[2026-05-27T23:58:17] Marking multi-mapping alignments (marked=2308173)
[2026-05-27T23:58:19] Detecting strandedness (reverse)
[2026-05-27T23:58:19] Assigning strands to alignments 
[2026-05-27T23:58:20] Annotating alignments 
[2026-05-27T23:58:32] Filtering duplicates (remaining=1621931)
[2026-05-27T23:58:34] 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=1532783)
[2026-05-27T23:58:35] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1532783)
[2026-05-27T23:58:36] Filtering viral contigs with expression lower than the top 5 (remaining=1532783)
[2026-05-27T23:58:37] Filtering viral contigs with less than 5% coverage (remaining=1532783)
[2026-05-27T23:58:38] Estimating fragment length (mate gap mean=-86.2816, mate gap stddev=28.0338, read length mean=128.213)
[2026-05-27T23:58:38] Filtering read-through fragments with a distance <=10000bp (remaining=1447687)
[2026-05-27T23:58:39] Filtering inconsistently clipped mates (remaining=1420885)
[2026-05-27T23:58:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1371817)
[2026-05-27T23:58:41] Filtering fragments with small insert size (remaining=1371525)
[2026-05-27T23:58:42] Filtering alignments with long gaps (remaining=1371525)
[2026-05-27T23:58:43] Filtering fragments with both mates in the same gene (remaining=1371166)
[2026-05-27T23:58:43] Filtering fusions arising from hairpin structures (remaining=1306797)
[2026-05-27T23:58:44] Filtering reads with a mismatch p-value <=0.01 (remaining=535841)
[2026-05-27T23:58:47] Filtering reads with low entropy (k-mer content >=60%) (remaining=208501)
[2026-05-27T23:58:50] Finding fusions and counting supporting reads (total=188970)
[2026-05-27T23:58:56] Merging adjacent fusion breakpoints (remaining=187761)
[2026-05-27T23:58:56] Filtering multi-mapping fusions by alignment score and read support (remaining=116343)
[2026-05-27T23:59:08] Estimating expected number of fusions by random chance (e-value) 
[2026-05-27T23:59:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=115630)
[2026-05-27T23:59:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=60389)
[2026-05-27T23:59:11] Filtering fusions with <2 supporting reads (remaining=5992)
[2026-05-27T23:59:11] Filtering fusions with an e-value >=0.3 (remaining=1775)
[2026-05-27T23:59:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1800)
[2026-05-27T23:59:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1778)
[2026-05-27T23:59:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1778)
[2026-05-27T23:59:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1652)
[2026-05-27T23:59:15] Searching for fusions with spliced split reads (remaining=1739)
[2026-05-27T23:59:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=1335)
[2026-05-27T23:59:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1323)
[2026-05-27T23:59:17] Searching for fusions with >=4 spliced events (remaining=1389)
[2026-05-27T23:59:17] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=365)
[2026-05-27T23:59:28] Filtering fusions with anchors <=23nt (remaining=295)
[2026-05-27T23:59:28] Filtering end-to-end fusions with low support (remaining=286)
[2026-05-27T23:59:29] Filtering fusions with no coverage around the breakpoints (remaining=277)
[2026-05-27T23:59:29] Indexing gene sequences 
[2026-05-27T23:59:31] Filtering genes with >=30% identity (remaining=127)
[2026-05-27T23:59:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=82)
[2026-05-27T23:59:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=81)
[2026-05-27T23:59:32] Searching for additional isoforms (remaining=88)
[2026-05-27T23:59:33] Assigning confidence scores to events 
[2026-05-27T23:59:34] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-27T23:59:34] Writing fusions to file '659_bGc-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-27T23:59:35] Writing discarded fusions to file '659_bGc-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-27T23:59:47] Freeing resources
[2026-05-27T23:59:57] Done (elapsed time=00:03:59, CPU time=00:03:58, peak memory=7.84gb)