[2026-06-08T08:27:49] Launching Arriba 2.4.0
[2026-06-08T08:27:49] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:28:01] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:28:05] Reading chimeric alignments from '659_1q-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10386377)
[2026-06-08T08:34:41] Marking multi-mapping alignments (marked=6481642)
[2026-06-08T08:34:45] Detecting strandedness (reverse)
[2026-06-08T08:34:45] Assigning strands to alignments 
[2026-06-08T08:34:47] Annotating alignments 
[2026-06-08T08:35:17] Filtering duplicates (remaining=7249191)
[2026-06-08T08:35:24] 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=6904383)
[2026-06-08T08:35:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6904383)
[2026-06-08T08:35:28] Filtering viral contigs with expression lower than the top 5 (remaining=6904383)
[2026-06-08T08:35:32] Filtering viral contigs with less than 5% coverage (remaining=6904383)
[2026-06-08T08:35:34] Estimating fragment length (mate gap mean=-84.0556, mate gap stddev=29.1836, read length mean=128.461)
[2026-06-08T08:35:34] Filtering read-through fragments with a distance <=10000bp (remaining=6534119)
[2026-06-08T08:35:36] Filtering inconsistently clipped mates (remaining=6439800)
[2026-06-08T08:35:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6295558)
[2026-06-08T08:35:42] Filtering fragments with small insert size (remaining=6294406)
[2026-06-08T08:35:43] Filtering alignments with long gaps (remaining=6294406)
[2026-06-08T08:35:45] Filtering fragments with both mates in the same gene (remaining=6293231)
[2026-06-08T08:35:47] Filtering fusions arising from hairpin structures (remaining=5980141)
[2026-06-08T08:35:49] Filtering reads with a mismatch p-value <=0.01 (remaining=3234237)
[2026-06-08T08:36:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=1243874)
[2026-06-08T08:36:16] Finding fusions and counting supporting reads (total=880008)
[2026-06-08T08:36:31] Merging adjacent fusion breakpoints (remaining=872241)
[2026-06-08T08:36:32] Filtering multi-mapping fusions by alignment score and read support (remaining=553769)
[2026-06-08T08:37:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:37:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=552327)
[2026-06-08T08:37:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=351784)
[2026-06-08T08:37:11] Filtering fusions with <2 supporting reads (remaining=38003)
[2026-06-08T08:37:12] Filtering fusions with an e-value >=0.3 (remaining=9727)
[2026-06-08T08:37:12] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9775)
[2026-06-08T08:37:16] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9693)
[2026-06-08T08:37:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9865)
[2026-06-08T08:37:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7766)
[2026-06-08T08:37:23] Searching for fusions with spliced split reads (remaining=7792)
[2026-06-08T08:37:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=4710)
[2026-06-08T08:37:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4666)
[2026-06-08T08:37:30] Searching for fusions with >=4 spliced events (remaining=5713)
[2026-06-08T08:37:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2445)
[2026-06-08T08:37:45] Filtering fusions with anchors <=23nt (remaining=1855)
[2026-06-08T08:37:46] Filtering end-to-end fusions with low support (remaining=1819)
[2026-06-08T08:37:47] Filtering fusions with no coverage around the breakpoints (remaining=1774)
[2026-06-08T08:37:47] Indexing gene sequences 
[2026-06-08T08:37:53] Filtering genes with >=30% identity (remaining=510)
[2026-06-08T08:37:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=211)
[2026-06-08T08:37:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=184)
[2026-06-08T08:37:59] Searching for additional isoforms (remaining=263)
[2026-06-08T08:38:01] Assigning confidence scores to events 
[2026-06-08T08:38:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:38:04] Writing fusions to file '659_1q-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:38:06] Writing discarded fusions to file '659_1q-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:38:35] Freeing resources
[2026-06-08T08:38:52] Done (elapsed time=00:11:03, CPU time=00:11:03, peak memory=14.9gb)