[2026-06-08T08:46:18] Launching Arriba 2.4.0
[2026-06-08T08:46:18] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:26] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:46:30] Reading chimeric alignments from '659_cTi-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10399288)
[2026-06-08T08:53:10] Marking multi-mapping alignments (marked=6311049)
[2026-06-08T08:53:15] Detecting strandedness (reverse)
[2026-06-08T08:53:15] Assigning strands to alignments 
[2026-06-08T08:53:17] Annotating alignments 
[2026-06-08T08:53:55] Filtering duplicates (remaining=4110120)
[2026-06-08T08:54:01] 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=3956858)
[2026-06-08T08:54:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3956858)
[2026-06-08T08:54:06] Filtering viral contigs with expression lower than the top 5 (remaining=3956858)
[2026-06-08T08:54:11] Filtering viral contigs with less than 5% coverage (remaining=3956858)
[2026-06-08T08:54:14] Estimating fragment length (mate gap mean=-87.164, mate gap stddev=28.3142, read length mean=130.757)
[2026-06-08T08:54:14] Filtering read-through fragments with a distance <=10000bp (remaining=3698850)
[2026-06-08T08:54:16] Filtering inconsistently clipped mates (remaining=3643195)
[2026-06-08T08:54:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3522891)
[2026-06-08T08:54:23] Filtering fragments with small insert size (remaining=3522296)
[2026-06-08T08:54:25] Filtering alignments with long gaps (remaining=3522296)
[2026-06-08T08:54:28] Filtering fragments with both mates in the same gene (remaining=3521480)
[2026-06-08T08:54:30] Filtering fusions arising from hairpin structures (remaining=3372129)
[2026-06-08T08:54:33] Filtering reads with a mismatch p-value <=0.01 (remaining=1401515)
[2026-06-08T08:54:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=564724)
[2026-06-08T08:54:51] Finding fusions and counting supporting reads (total=476450)
[2026-06-08T08:55:07] Merging adjacent fusion breakpoints (remaining=470564)
[2026-06-08T08:55:08] Filtering multi-mapping fusions by alignment score and read support (remaining=301449)
[2026-06-08T08:55:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:55:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=299901)
[2026-06-08T08:55:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=145450)
[2026-06-08T08:55:52] Filtering fusions with <2 supporting reads (remaining=19054)
[2026-06-08T08:55:52] Filtering fusions with an e-value >=0.3 (remaining=5587)
[2026-06-08T08:55:53] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5612)
[2026-06-08T08:55:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5518)
[2026-06-08T08:55:57] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5518)
[2026-06-08T08:55:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4684)
[2026-06-08T08:56:03] Searching for fusions with spliced split reads (remaining=4755)
[2026-06-08T08:56:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=3276)
[2026-06-08T08:56:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3221)
[2026-06-08T08:56:10] Searching for fusions with >=4 spliced events (remaining=3672)
[2026-06-08T08:56:11] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1259)
[2026-06-08T08:56:26] Filtering fusions with anchors <=23nt (remaining=954)
[2026-06-08T08:56:26] Filtering end-to-end fusions with low support (remaining=928)
[2026-06-08T08:56:27] Filtering fusions with no coverage around the breakpoints (remaining=902)
[2026-06-08T08:56:27] Indexing gene sequences 
[2026-06-08T08:56:31] Filtering genes with >=30% identity (remaining=316)
[2026-06-08T08:56:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=150)
[2026-06-08T08:56:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=134)
[2026-06-08T08:56:36] Searching for additional isoforms (remaining=161)
[2026-06-08T08:56:37] Assigning confidence scores to events 
[2026-06-08T08:56:40] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:56:40] Writing fusions to file '659_cTi-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:56:41] Writing discarded fusions to file '659_cTi-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:57:06] Freeing resources
[2026-06-08T08:57:26] Done (elapsed time=00:11:08, CPU time=00:11:08, peak memory=14.8gb)