[2026-06-08T08:48:47] Launching Arriba 2.4.0
[2026-06-08T08:48:47] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:03] Reading chimeric alignments from '659_eGK-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10549182)
[2026-06-08T08:56:02] Marking multi-mapping alignments (marked=6381936)
[2026-06-08T08:56:06] Detecting strandedness (reverse)
[2026-06-08T08:56:06] Assigning strands to alignments 
[2026-06-08T08:56:08] Annotating alignments 
[2026-06-08T08:56:40] Filtering duplicates (remaining=7907530)
[2026-06-08T08:56:47] 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=7538822)
[2026-06-08T08:56:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7538822)
[2026-06-08T08:56:51] Filtering viral contigs with expression lower than the top 5 (remaining=7538822)
[2026-06-08T08:56:56] Filtering viral contigs with less than 5% coverage (remaining=7538822)
[2026-06-08T08:56:58] Estimating fragment length (mate gap mean=-84.5326, mate gap stddev=30.5458, read length mean=134.69)
[2026-06-08T08:56:58] Filtering read-through fragments with a distance <=10000bp (remaining=7168992)
[2026-06-08T08:57:00] Filtering inconsistently clipped mates (remaining=7069358)
[2026-06-08T08:57:02] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6902582)
[2026-06-08T08:57:06] Filtering fragments with small insert size (remaining=6901599)
[2026-06-08T08:57:08] Filtering alignments with long gaps (remaining=6901599)
[2026-06-08T08:57:10] Filtering fragments with both mates in the same gene (remaining=6900302)
[2026-06-08T08:57:12] Filtering fusions arising from hairpin structures (remaining=6507887)
[2026-06-08T08:57:15] Filtering reads with a mismatch p-value <=0.01 (remaining=3648849)
[2026-06-08T08:57:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=1564374)
[2026-06-08T08:57:46] Finding fusions and counting supporting reads (total=1179580)
[2026-06-08T08:58:03] Merging adjacent fusion breakpoints (remaining=1171979)
[2026-06-08T08:58:05] Filtering multi-mapping fusions by alignment score and read support (remaining=752268)
[2026-06-08T08:58:35] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:43] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=748837)
[2026-06-08T08:58:44] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=484454)
[2026-06-08T08:58:45] Filtering fusions with <2 supporting reads (remaining=48195)
[2026-06-08T08:58:46] Filtering fusions with an e-value >=0.3 (remaining=13446)
[2026-06-08T08:58:47] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13504)
[2026-06-08T08:58:51] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13420)
[2026-06-08T08:58:51] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13429)
[2026-06-08T08:58:53] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9430)
[2026-06-08T08:58:58] Searching for fusions with spliced split reads (remaining=9482)
[2026-06-08T08:59:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=4954)
[2026-06-08T08:59:05] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4895)
[2026-06-08T08:59:06] Searching for fusions with >=4 spliced events (remaining=6115)
[2026-06-08T08:59:07] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2219)
[2026-06-08T08:59:21] Filtering fusions with anchors <=23nt (remaining=1742)
[2026-06-08T08:59:22] Filtering end-to-end fusions with low support (remaining=1700)
[2026-06-08T08:59:23] Filtering fusions with no coverage around the breakpoints (remaining=1646)
[2026-06-08T08:59:23] Indexing gene sequences 
[2026-06-08T08:59:30] Filtering genes with >=30% identity (remaining=518)
[2026-06-08T08:59:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=284)
[2026-06-08T08:59:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=257)
[2026-06-08T08:59:48] Searching for additional isoforms (remaining=338)
[2026-06-08T08:59:49] Assigning confidence scores to events 
[2026-06-08T08:59:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:53] Writing fusions to file '659_eGK-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:56] Writing discarded fusions to file '659_eGK-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:30] Freeing resources
[2026-06-08T09:00:48] Done (elapsed time=00:12:01, CPU time=00:12:00, peak memory=15.2gb)