[2026-06-08T08:50:32] Launching Arriba 2.4.0
[2026-06-08T08:50:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:50:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:50:47] Reading chimeric alignments from '659_cfy-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9441657)
[2026-06-08T08:57:55] Marking multi-mapping alignments (marked=5724055)
[2026-06-08T08:57:59] Detecting strandedness (no)
[2026-06-08T08:57:59] Annotating alignments 
[2026-06-08T08:58:40] Filtering duplicates (remaining=4336219)
[2026-06-08T08:58:45] 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=4128348)
[2026-06-08T08:58:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4128348)
[2026-06-08T08:58:49] Filtering viral contigs with expression lower than the top 5 (remaining=4128348)
[2026-06-08T08:58:53] Filtering viral contigs with less than 5% coverage (remaining=4128348)
[2026-06-08T08:58:55] Estimating fragment length (mate gap mean=-88.2023, mate gap stddev=28.6802, read length mean=134.404)
[2026-06-08T08:58:55] Filtering read-through fragments with a distance <=10000bp (remaining=3869981)
[2026-06-08T08:58:57] Filtering inconsistently clipped mates (remaining=3810957)
[2026-06-08T08:58:59] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3677236)
[2026-06-08T08:59:02] Filtering fragments with small insert size (remaining=3676678)
[2026-06-08T08:59:04] Filtering alignments with long gaps (remaining=3676678)
[2026-06-08T08:59:06] Filtering fragments with both mates in the same gene (remaining=3676016)
[2026-06-08T08:59:08] Filtering fusions arising from hairpin structures (remaining=3484756)
[2026-06-08T08:59:10] Filtering reads with a mismatch p-value <=0.01 (remaining=1518334)
[2026-06-08T08:59:21] Filtering reads with low entropy (k-mer content >=60%) (remaining=600923)
[2026-06-08T08:59:28] Finding fusions and counting supporting reads (total=496914)
[2026-06-08T08:59:42] Merging adjacent fusion breakpoints (remaining=491396)
[2026-06-08T08:59:44] Filtering multi-mapping fusions by alignment score and read support (remaining=323982)
[2026-06-08T09:00:15] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=322579)
[2026-06-08T09:00:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=159509)
[2026-06-08T09:00:23] Filtering fusions with <2 supporting reads (remaining=22582)
[2026-06-08T09:00:24] Filtering fusions with an e-value >=0.3 (remaining=7128)
[2026-06-08T09:00:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7157)
[2026-06-08T09:00:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7101)
[2026-06-08T09:00:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7137)
[2026-06-08T09:00:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4892)
[2026-06-08T09:00:36] Searching for fusions with spliced split reads (remaining=4964)
[2026-06-08T09:00:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=3252)
[2026-06-08T09:00:41] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3208)
[2026-06-08T09:00:41] Searching for fusions with >=4 spliced events (remaining=3792)
[2026-06-08T09:00:43] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1377)
[2026-06-08T09:00:57] Filtering fusions with anchors <=23nt (remaining=1085)
[2026-06-08T09:00:57] Filtering end-to-end fusions with low support (remaining=1056)
[2026-06-08T09:00:58] Filtering fusions with no coverage around the breakpoints (remaining=1036)
[2026-06-08T09:00:58] Indexing gene sequences 
[2026-06-08T09:01:03] Filtering genes with >=30% identity (remaining=345)
[2026-06-08T09:01:05] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=152)
[2026-06-08T09:01:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=138)
[2026-06-08T09:01:08] Searching for additional isoforms (remaining=160)
[2026-06-08T09:01:09] Assigning confidence scores to events 
[2026-06-08T09:01:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:12] Writing fusions to file '659_cfy-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:01:13] Writing discarded fusions to file '659_cfy-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:37] Freeing resources
[2026-06-08T09:01:54] Done (elapsed time=00:11:22, CPU time=00:11:20, peak memory=14gb)