[2026-06-04T21:09:46] Launching Arriba 2.4.0
[2026-06-04T21:09:46] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:09:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:09:58] Reading chimeric alignments from '659_dKM-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10782533)
[2026-06-04T21:16:40] Marking multi-mapping alignments (marked=6699122)
[2026-06-04T21:16:45] Detecting strandedness (reverse)
[2026-06-04T21:16:45] Assigning strands to alignments 
[2026-06-04T21:16:47] Annotating alignments 
[2026-06-04T21:17:22] Filtering duplicates (remaining=6965957)
[2026-06-04T21:17:29] 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)
[2026-06-04T21:17:31] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6609727)
[2026-06-04T21:17:34] Filtering viral contigs with expression lower than the top 5 (remaining=6609727)
[2026-06-04T21:17:39] Filtering viral contigs with less than 5% coverage (remaining=6609727)
[2026-06-04T21:17:41] Estimating fragment length (mate gap mean=-87.476, mate gap stddev=27.6882, read length mean=129.575)
[2026-06-04T21:17:42] Filtering read-through fragments with a distance <=10000bp (remaining=6128461)
[2026-06-04T21:17:44] Filtering inconsistently clipped mates (remaining=6042698)
[2026-06-04T21:17:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5809242)
[2026-06-04T21:17:51] Filtering fragments with small insert size (remaining=5808199)
[2026-06-04T21:17:53] Filtering alignments with long gaps (remaining=5808199)
[2026-06-04T21:17:56] Filtering fragments with both mates in the same gene (remaining=5807291)
[2026-06-04T21:17:58] Filtering fusions arising from hairpin structures (remaining=5533169)
[2026-06-04T21:18:01] Filtering reads with a mismatch p-value <=0.01 (remaining=2860200)
[2026-06-04T21:18:15] Filtering reads with low entropy (k-mer content >=60%) (remaining=1433460)
[2026-06-04T21:18:27] Finding fusions and counting supporting reads (total=1022024)
[2026-06-04T21:18:44] Merging adjacent fusion breakpoints (remaining=1010061)
[2026-06-04T21:18:46] Filtering multi-mapping fusions by alignment score and read support (remaining=619633)
[2026-06-04T21:19:19] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:19:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=618097)
[2026-06-04T21:19:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=349052)
[2026-06-04T21:19:29] Filtering fusions with <2 supporting reads (remaining=48901)
[2026-06-04T21:19:30] Filtering fusions with an e-value >=0.3 (remaining=10600)
[2026-06-04T21:19:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10638)
[2026-06-04T21:19:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10522)
[2026-06-04T21:19:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10522)
[2026-06-04T21:19:37] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9728)
[2026-06-04T21:19:42] Searching for fusions with spliced split reads (remaining=9851)
[2026-06-04T21:19:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=5814)
[2026-06-04T21:19:49] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5765)
[2026-06-04T21:19:50] Searching for fusions with >=4 spliced events (remaining=7420)
[2026-06-04T21:19:52] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3032)
[2026-06-04T21:20:06] Filtering fusions with anchors <=23nt (remaining=2538)
[2026-06-04T21:20:07] Filtering end-to-end fusions with low support (remaining=2487)
[2026-06-04T21:20:07] Filtering fusions with no coverage around the breakpoints (remaining=2413)
[2026-06-04T21:20:08] Indexing gene sequences 
[2026-06-04T21:20:15] Filtering genes with >=30% identity (remaining=757)
[2026-06-04T21:20:19] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=370)
[2026-06-04T21:20:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=273)
[2026-06-04T21:20:25] Searching for additional isoforms (remaining=397)
[2026-06-04T21:20:26] Assigning confidence scores to events 
[2026-06-04T21:20:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:20:30] Writing fusions to file '659_dKM-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:20:33] Writing discarded fusions to file '659_dKM-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:21:02] Freeing resources
[2026-06-04T21:21:21] Done (elapsed time=00:11:35, CPU time=00:11:33, peak memory=15.6gb)