[2026-06-04T21:01:22] Launching Arriba 2.4.0
[2026-06-04T21:01:22] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:01:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:01:33] Reading chimeric alignments from '659_rd-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=6674662)
[2026-06-04T21:06:09] Marking multi-mapping alignments (marked=3802746)
[2026-06-04T21:06:11] Detecting strandedness (reverse)
[2026-06-04T21:06:11] Assigning strands to alignments 
[2026-06-04T21:06:13] Annotating alignments 
[2026-06-04T21:06:33] Filtering duplicates (remaining=4808826)
[2026-06-04T21:06:37] 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=4569275)
[2026-06-04T21:06:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4569275)
[2026-06-04T21:06:40] Filtering viral contigs with expression lower than the top 5 (remaining=4569275)
[2026-06-04T21:06:43] Filtering viral contigs with less than 5% coverage (remaining=4569275)
[2026-06-04T21:06:44] Estimating fragment length (mate gap mean=-85.5334, mate gap stddev=30.4011, read length mean=137.071)
[2026-06-04T21:06:44] Filtering read-through fragments with a distance <=10000bp (remaining=4253360)
[2026-06-04T21:06:46] Filtering inconsistently clipped mates (remaining=4201251)
[2026-06-04T21:06:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4070984)
[2026-06-04T21:06:50] Filtering fragments with small insert size (remaining=4070481)
[2026-06-04T21:06:51] Filtering alignments with long gaps (remaining=4070481)
[2026-06-04T21:06:53] Filtering fragments with both mates in the same gene (remaining=4069586)
[2026-06-04T21:06:54] Filtering fusions arising from hairpin structures (remaining=3876275)
[2026-06-04T21:06:56] Filtering reads with a mismatch p-value <=0.01 (remaining=2234571)
[2026-06-04T21:07:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=1072330)
[2026-06-04T21:07:14] Finding fusions and counting supporting reads (total=655950)
[2026-06-04T21:07:24] Merging adjacent fusion breakpoints (remaining=651496)
[2026-06-04T21:07:25] Filtering multi-mapping fusions by alignment score and read support (remaining=445076)
[2026-06-04T21:07:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:07:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=442939)
[2026-06-04T21:07:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=246340)
[2026-06-04T21:07:50] Filtering fusions with <2 supporting reads (remaining=42631)
[2026-06-04T21:07:51] Filtering fusions with an e-value >=0.3 (remaining=13219)
[2026-06-04T21:07:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13261)
[2026-06-04T21:07:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13211)
[2026-06-04T21:07:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13256)
[2026-06-04T21:07:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9244)
[2026-06-04T21:07:59] Searching for fusions with spliced split reads (remaining=9303)
[2026-06-04T21:08:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=4914)
[2026-06-04T21:08:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4858)
[2026-06-04T21:08:03] Searching for fusions with >=4 spliced events (remaining=5912)
[2026-06-04T21:08:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1824)
[2026-06-04T21:08:16] Filtering fusions with anchors <=23nt (remaining=1525)
[2026-06-04T21:08:17] Filtering end-to-end fusions with low support (remaining=1480)
[2026-06-04T21:08:17] Filtering fusions with no coverage around the breakpoints (remaining=1448)
[2026-06-04T21:08:18] Indexing gene sequences 
[2026-06-04T21:08:23] Filtering genes with >=30% identity (remaining=441)
[2026-06-04T21:08:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=223)
[2026-06-04T21:08:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=200)
[2026-06-04T21:08:39] Searching for additional isoforms (remaining=267)
[2026-06-04T21:08:40] Assigning confidence scores to events 
[2026-06-04T21:08:43] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:08:43] Writing fusions to file '659_rd-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:08:45] Writing discarded fusions to file '659_rd-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:09:03] Freeing resources
[2026-06-04T21:09:15] Done (elapsed time=00:07:53, CPU time=00:07:52, peak memory=11.2gb)