[2026-06-08T08:45:44] Launching Arriba 2.4.0
[2026-06-08T08:45:44] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:45:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:46:00] Reading chimeric alignments from '659_cRa-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9340394)
[2026-06-08T08:53:34] Marking multi-mapping alignments (marked=5654125)
[2026-06-08T08:53:39] Detecting strandedness (no)
[2026-06-08T08:53:39] Annotating alignments 
[2026-06-08T08:54:20] Filtering duplicates (remaining=3810025)
[2026-06-08T08:54:26] 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=3662581)
[2026-06-08T08:54:28] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3662581)
[2026-06-08T08:54:30] Filtering viral contigs with expression lower than the top 5 (remaining=3662581)
[2026-06-08T08:54:34] Filtering viral contigs with less than 5% coverage (remaining=3662581)
[2026-06-08T08:54:37] Estimating fragment length (mate gap mean=-86.9529, mate gap stddev=30.0534, read length mean=135.012)
[2026-06-08T08:54:37] Filtering read-through fragments with a distance <=10000bp (remaining=3458824)
[2026-06-08T08:54:39] Filtering inconsistently clipped mates (remaining=3400323)
[2026-06-08T08:54:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3281947)
[2026-06-08T08:54:44] Filtering fragments with small insert size (remaining=3281265)
[2026-06-08T08:54:46] Filtering alignments with long gaps (remaining=3281265)
[2026-06-08T08:54:48] Filtering fragments with both mates in the same gene (remaining=3280579)
[2026-06-08T08:54:51] Filtering fusions arising from hairpin structures (remaining=3101439)
[2026-06-08T08:54:53] Filtering reads with a mismatch p-value <=0.01 (remaining=1325596)
[2026-06-08T08:55:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=527043)
[2026-06-08T08:55:10] Finding fusions and counting supporting reads (total=420190)
[2026-06-08T08:55:25] Merging adjacent fusion breakpoints (remaining=415170)
[2026-06-08T08:55:26] Filtering multi-mapping fusions by alignment score and read support (remaining=262986)
[2026-06-08T08:55:59] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:56:04] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=261006)
[2026-06-08T08:56:04] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=132110)
[2026-06-08T08:56:05] Filtering fusions with <2 supporting reads (remaining=20180)
[2026-06-08T08:56:05] Filtering fusions with an e-value >=0.3 (remaining=6798)
[2026-06-08T08:56:06] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6841)
[2026-06-08T08:56:09] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6730)
[2026-06-08T08:56:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6730)
[2026-06-08T08:56:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4055)
[2026-06-08T08:56:15] Searching for fusions with spliced split reads (remaining=4152)
[2026-06-08T08:56:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=2836)
[2026-06-08T08:56:20] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2799)
[2026-06-08T08:56:21] Searching for fusions with >=4 spliced events (remaining=3164)
[2026-06-08T08:56:22] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1042)
[2026-06-08T08:56:36] Filtering fusions with anchors <=23nt (remaining=804)
[2026-06-08T08:56:36] Filtering end-to-end fusions with low support (remaining=782)
[2026-06-08T08:56:37] Filtering fusions with no coverage around the breakpoints (remaining=756)
[2026-06-08T08:56:37] Indexing gene sequences 
[2026-06-08T08:56:41] Filtering genes with >=30% identity (remaining=244)
[2026-06-08T08:56:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=118)
[2026-06-08T08:56:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=108)
[2026-06-08T08:56:45] Searching for additional isoforms (remaining=130)
[2026-06-08T08:56:46] Assigning confidence scores to events 
[2026-06-08T08:56:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:56:49] Writing fusions to file '659_cRa-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:56:50] Writing discarded fusions to file '659_cRa-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:57:10] Freeing resources
[2026-06-08T08:57:27] Done (elapsed time=00:11:43, CPU time=00:11:42, peak memory=13.7gb)