[2026-06-04T21:19:42] Launching Arriba 2.4.0
[2026-06-04T21:19:42] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:19:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:19:54] Reading chimeric alignments from '659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10976796)
[2026-06-04T21:26:54] Marking multi-mapping alignments (marked=6809750)
[2026-06-04T21:26:59] Detecting strandedness (reverse)
[2026-06-04T21:26:59] Assigning strands to alignments 
[2026-06-04T21:27:01] Annotating alignments 
[2026-06-04T21:27:32] Filtering duplicates (remaining=5768000)
[2026-06-04T21:27:38] 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=5370199)
[2026-06-04T21:27:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5370199)
[2026-06-04T21:27:42] Filtering viral contigs with expression lower than the top 5 (remaining=5370199)
[2026-06-04T21:27:47] Filtering viral contigs with less than 5% coverage (remaining=5370199)
[2026-06-04T21:27:49] Estimating fragment length (mate gap mean=-88.2308, mate gap stddev=27.2718, read length mean=133.491)
[2026-06-04T21:27:49] Filtering read-through fragments with a distance <=10000bp (remaining=4995314)
[2026-06-04T21:27:51] Filtering inconsistently clipped mates (remaining=4877197)
[2026-06-04T21:27:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4740030)
[2026-06-04T21:27:57] Filtering fragments with small insert size (remaining=4738773)
[2026-06-04T21:27:59] Filtering alignments with long gaps (remaining=4738773)
[2026-06-04T21:28:02] Filtering fragments with both mates in the same gene (remaining=4737947)
[2026-06-04T21:28:04] Filtering fusions arising from hairpin structures (remaining=4338189)
[2026-06-04T21:28:06] Filtering reads with a mismatch p-value <=0.01 (remaining=2266466)
[2026-06-04T21:28:18] Filtering reads with low entropy (k-mer content >=60%) (remaining=995271)
[2026-06-04T21:28:28] Finding fusions and counting supporting reads (total=705512)
[2026-06-04T21:28:42] Merging adjacent fusion breakpoints (remaining=694992)
[2026-06-04T21:28:43] Filtering multi-mapping fusions by alignment score and read support (remaining=455931)
[2026-06-04T21:29:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:29:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=453846)
[2026-06-04T21:29:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=229343)
[2026-06-04T21:29:20] Filtering fusions with <2 supporting reads (remaining=30572)
[2026-06-04T21:29:20] Filtering fusions with an e-value >=0.3 (remaining=8015)
[2026-06-04T21:29:21] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8110)
[2026-06-04T21:29:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8031)
[2026-06-04T21:29:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8031)
[2026-06-04T21:29:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5534)
[2026-06-04T21:29:31] Searching for fusions with spliced split reads (remaining=5620)
[2026-06-04T21:29:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=3742)
[2026-06-04T21:29:36] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3695)
[2026-06-04T21:29:37] Searching for fusions with >=4 spliced events (remaining=4236)
[2026-06-04T21:29:38] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1436)
[2026-06-04T21:29:51] Filtering fusions with anchors <=23nt (remaining=1128)
[2026-06-04T21:29:51] Filtering end-to-end fusions with low support (remaining=1104)
[2026-06-04T21:29:52] Filtering fusions with no coverage around the breakpoints (remaining=1074)
[2026-06-04T21:29:52] Indexing gene sequences 
[2026-06-04T21:29:56] Filtering genes with >=30% identity (remaining=421)
[2026-06-04T21:29:58] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=190)
[2026-06-04T21:30:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=176)
[2026-06-04T21:30:02] Searching for additional isoforms (remaining=207)
[2026-06-04T21:30:03] Assigning confidence scores to events 
[2026-06-04T21:30:06] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:30:06] Writing fusions to file '659_eHw-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:30:07] Writing discarded fusions to file '659_eHw-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:30:29] Freeing resources
[2026-06-04T21:30:47] Done (elapsed time=00:11:05, CPU time=00:11:04, peak memory=15.7gb)