[2026-06-08T08:29:18] Launching Arriba 2.4.0
[2026-06-08T08:29:18] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:29:26] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:29:30] Reading chimeric alignments from '659_Mt-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=9121492)
[2026-06-08T08:34:29] Marking multi-mapping alignments (marked=5737603)
[2026-06-08T08:34:33] Detecting strandedness (reverse)
[2026-06-08T08:34:33] Assigning strands to alignments 
[2026-06-08T08:34:34] Annotating alignments 
[2026-06-08T08:35:02] Filtering duplicates (remaining=4727550)
[2026-06-08T08:35:07] 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=4573433)
[2026-06-08T08:35:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4573433)
[2026-06-08T08:35:10] Filtering viral contigs with expression lower than the top 5 (remaining=4573433)
[2026-06-08T08:35:14] Filtering viral contigs with less than 5% coverage (remaining=4573433)
[2026-06-08T08:35:16] Estimating fragment length (mate gap mean=-90.409, mate gap stddev=27.5365, read length mean=135.46)
[2026-06-08T08:35:16] Filtering read-through fragments with a distance <=10000bp (remaining=4292958)
[2026-06-08T08:35:18] Filtering inconsistently clipped mates (remaining=4205311)
[2026-06-08T08:35:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4063736)
[2026-06-08T08:35:23] Filtering fragments with small insert size (remaining=4063339)
[2026-06-08T08:35:24] Filtering alignments with long gaps (remaining=4063338)
[2026-06-08T08:35:26] Filtering fragments with both mates in the same gene (remaining=4062674)
[2026-06-08T08:35:28] Filtering fusions arising from hairpin structures (remaining=3797148)
[2026-06-08T08:35:30] Filtering reads with a mismatch p-value <=0.01 (remaining=1917443)
[2026-06-08T08:35:41] Filtering reads with low entropy (k-mer content >=60%) (remaining=740009)
[2026-06-08T08:35:49] Finding fusions and counting supporting reads (total=535462)
[2026-06-08T08:36:02] Merging adjacent fusion breakpoints (remaining=529783)
[2026-06-08T08:36:03] Filtering multi-mapping fusions by alignment score and read support (remaining=307080)
[2026-06-08T08:36:31] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:36:37] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=305819)
[2026-06-08T08:36:37] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=177753)
[2026-06-08T08:36:38] Filtering fusions with <2 supporting reads (remaining=25343)
[2026-06-08T08:36:39] Filtering fusions with an e-value >=0.3 (remaining=6154)
[2026-06-08T08:36:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6208)
[2026-06-08T08:36:43] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6107)
[2026-06-08T08:36:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6107)
[2026-06-08T08:36:44] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5380)
[2026-06-08T08:36:48] Searching for fusions with spliced split reads (remaining=5500)
[2026-06-08T08:36:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=3673)
[2026-06-08T08:36:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3626)
[2026-06-08T08:36:54] Searching for fusions with >=4 spliced events (remaining=4250)
[2026-06-08T08:36:55] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1491)
[2026-06-08T08:37:07] Filtering fusions with anchors <=23nt (remaining=1280)
[2026-06-08T08:37:08] Filtering end-to-end fusions with low support (remaining=1235)
[2026-06-08T08:37:08] Filtering fusions with no coverage around the breakpoints (remaining=1205)
[2026-06-08T08:37:09] Indexing gene sequences 
[2026-06-08T08:37:14] Filtering genes with >=30% identity (remaining=351)
[2026-06-08T08:37:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=159)
[2026-06-08T08:37:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=151)
[2026-06-08T08:37:20] Searching for additional isoforms (remaining=190)
[2026-06-08T08:37:21] Assigning confidence scores to events 
[2026-06-08T08:37:24] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:37:24] Writing fusions to file '659_Mt-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:37:25] Writing discarded fusions to file '659_Mt-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:37:46] Freeing resources
[2026-06-08T08:38:02] Done (elapsed time=00:08:44, CPU time=00:08:43, peak memory=13.5gb)