[2026-06-08T08:22:49] Launching Arriba 2.4.0
[2026-06-08T08:22:49] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:22:58] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:23:02] Reading chimeric alignments from '659_dKM-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10782533)
[2026-06-08T08:29:43] Marking multi-mapping alignments (marked=6699122)
[2026-06-08T08:29:47] Detecting strandedness (reverse)
[2026-06-08T08:29:47] Assigning strands to alignments 
[2026-06-08T08:29:49] Annotating alignments 
[2026-06-08T08:30:24] Filtering duplicates (remaining=6965957)
[2026-06-08T08:30:31] 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=6609727)
[2026-06-08T08:30:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6609727)
[2026-06-08T08:30:35] Filtering viral contigs with expression lower than the top 5 (remaining=6609727)
[2026-06-08T08:30:40] Filtering viral contigs with less than 5% coverage (remaining=6609727)
[2026-06-08T08:30:42] Estimating fragment length (mate gap mean=-87.476, mate gap stddev=27.6882, read length mean=129.575)
[2026-06-08T08:30:42] Filtering read-through fragments with a distance <=10000bp (remaining=6128461)
[2026-06-08T08:30:44] Filtering inconsistently clipped mates (remaining=6042698)
[2026-06-08T08:30:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5809242)
[2026-06-08T08:30:51] Filtering fragments with small insert size (remaining=5808199)
[2026-06-08T08:30:53] Filtering alignments with long gaps (remaining=5808199)
[2026-06-08T08:30:55] Filtering fragments with both mates in the same gene (remaining=5807291)
[2026-06-08T08:30:57] Filtering fusions arising from hairpin structures (remaining=5533169)
[2026-06-08T08:31:00] Filtering reads with a mismatch p-value <=0.01 (remaining=2860200)
[2026-06-08T08:31:16] Filtering reads with low entropy (k-mer content >=60%) (remaining=1433460)
[2026-06-08T08:31:27] Finding fusions and counting supporting reads (total=1022024)
[2026-06-08T08:31:45] Merging adjacent fusion breakpoints (remaining=1010061)
[2026-06-08T08:31:46] Filtering multi-mapping fusions by alignment score and read support (remaining=619633)
[2026-06-08T08:32:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:32:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=618097)
[2026-06-08T08:32:29] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=349052)
[2026-06-08T08:32:30] Filtering fusions with <2 supporting reads (remaining=48901)
[2026-06-08T08:32:31] Filtering fusions with an e-value >=0.3 (remaining=10600)
[2026-06-08T08:32:32] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10638)
[2026-06-08T08:32:36] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10522)
[2026-06-08T08:32:37] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10522)
[2026-06-08T08:32:38] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9728)
[2026-06-08T08:32:43] Searching for fusions with spliced split reads (remaining=9851)
[2026-06-08T08:32:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=5814)
[2026-06-08T08:32:50] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5765)
[2026-06-08T08:32:51] Searching for fusions with >=4 spliced events (remaining=7420)
[2026-06-08T08:32:52] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3032)
[2026-06-08T08:33:06] Filtering fusions with anchors <=23nt (remaining=2538)
[2026-06-08T08:33:07] Filtering end-to-end fusions with low support (remaining=2487)
[2026-06-08T08:33:08] Filtering fusions with no coverage around the breakpoints (remaining=2413)
[2026-06-08T08:33:09] Indexing gene sequences 
[2026-06-08T08:33:16] Filtering genes with >=30% identity (remaining=757)
[2026-06-08T08:33:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=370)
[2026-06-08T08:33:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=273)
[2026-06-08T08:33:25] Searching for additional isoforms (remaining=397)
[2026-06-08T08:33:27] Assigning confidence scores to events 
[2026-06-08T08:33:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:33:30] Writing fusions to file '659_dKM-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:33:33] Writing discarded fusions to file '659_dKM-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:34:04] Freeing resources
[2026-06-08T08:34:21] Done (elapsed time=00:11:32, CPU time=00:11:30, peak memory=15.6gb)