[2026-06-08T08:29:51] Launching Arriba 2.4.0
[2026-06-08T08:29:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:29:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:30:03] Reading chimeric alignments from '659_epG-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10380268)
[2026-06-08T08:37:08] Marking multi-mapping alignments (marked=6816615)
[2026-06-08T08:37:13] Detecting strandedness (reverse)
[2026-06-08T08:37:13] Assigning strands to alignments 
[2026-06-08T08:37:15] Annotating alignments 
[2026-06-08T08:37:58] Filtering duplicates (remaining=6836419)
[2026-06-08T08:38:11] 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=6476463)
[2026-06-08T08:38:14] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6476463)
[2026-06-08T08:38:16] Filtering viral contigs with expression lower than the top 5 (remaining=6476463)
[2026-06-08T08:38:21] Filtering viral contigs with less than 5% coverage (remaining=6476463)
[2026-06-08T08:38:24] Estimating fragment length (mate gap mean=-87.3524, mate gap stddev=28.4725, read length mean=130.768)
[2026-06-08T08:38:24] Filtering read-through fragments with a distance <=10000bp (remaining=6058366)
[2026-06-08T08:38:26] Filtering inconsistently clipped mates (remaining=5934604)
[2026-06-08T08:38:29] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5777709)
[2026-06-08T08:38:34] Filtering fragments with small insert size (remaining=5777115)
[2026-06-08T08:38:36] Filtering alignments with long gaps (remaining=5777115)
[2026-06-08T08:38:38] Filtering fragments with both mates in the same gene (remaining=5776071)
[2026-06-08T08:38:41] Filtering fusions arising from hairpin structures (remaining=5346555)
[2026-06-08T08:38:44] Filtering reads with a mismatch p-value <=0.01 (remaining=2869237)
[2026-06-08T08:38:59] Filtering reads with low entropy (k-mer content >=60%) (remaining=1270057)
[2026-06-08T08:39:12] Finding fusions and counting supporting reads (total=847910)
[2026-06-08T08:39:30] Merging adjacent fusion breakpoints (remaining=839144)
[2026-06-08T08:39:31] Filtering multi-mapping fusions by alignment score and read support (remaining=491961)
[2026-06-08T08:40:07] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:40:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=489391)
[2026-06-08T08:40:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=295409)
[2026-06-08T08:40:16] Filtering fusions with <2 supporting reads (remaining=34231)
[2026-06-08T08:40:17] Filtering fusions with an e-value >=0.3 (remaining=8527)
[2026-06-08T08:40:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8589)
[2026-06-08T08:40:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8451)
[2026-06-08T08:40:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8458)
[2026-06-08T08:40:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7759)
[2026-06-08T08:40:29] Searching for fusions with spliced split reads (remaining=7785)
[2026-06-08T08:40:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=4841)
[2026-06-08T08:40:35] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4782)
[2026-06-08T08:40:36] Searching for fusions with >=4 spliced events (remaining=5639)
[2026-06-08T08:40:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2097)
[2026-06-08T08:40:50] Filtering fusions with anchors <=23nt (remaining=1725)
[2026-06-08T08:40:51] Filtering end-to-end fusions with low support (remaining=1668)
[2026-06-08T08:40:51] Filtering fusions with no coverage around the breakpoints (remaining=1627)
[2026-06-08T08:40:52] Indexing gene sequences 
[2026-06-08T08:40:58] Filtering genes with >=30% identity (remaining=554)
[2026-06-08T08:41:02] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=313)
[2026-06-08T08:41:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=245)
[2026-06-08T08:41:14] Searching for additional isoforms (remaining=322)
[2026-06-08T08:41:15] Assigning confidence scores to events 
[2026-06-08T08:41:19] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:41:20] Writing fusions to file '659_epG-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:41:22] Writing discarded fusions to file '659_epG-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:41:57] Freeing resources
[2026-06-08T08:42:21] Done (elapsed time=00:12:30, CPU time=00:12:29, peak memory=15gb)