[2026-06-04T20:58:32] Launching Arriba 2.4.0
[2026-06-04T20:58:32] Loading assembly from 'ref_genome.fa' 
[2026-06-04T20:58:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T20:58:43] Reading chimeric alignments from '659_Lx-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10985496)
[2026-06-04T21:04:31] Marking multi-mapping alignments (marked=7214932)
[2026-06-04T21:04:35] Detecting strandedness (no)
[2026-06-04T21:04:35] Annotating alignments 
[2026-06-04T21:05:22] Filtering duplicates (remaining=7388186)
[2026-06-04T21:05:30] 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=6703825)
[2026-06-04T21:05:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6703825)
[2026-06-04T21:05:34] Filtering viral contigs with expression lower than the top 5 (remaining=6703825)
[2026-06-04T21:05:39] Filtering viral contigs with less than 5% coverage (remaining=6703825)
[2026-06-04T21:05:42] Estimating fragment length (mate gap mean=-82.9972, mate gap stddev=27.5147, read length mean=121.308)
[2026-06-04T21:05:42] Filtering read-through fragments with a distance <=10000bp (remaining=6300067)
[2026-06-04T21:05:44] Filtering inconsistently clipped mates (remaining=6204411)
[2026-06-04T21:05:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6053435)
[2026-06-04T21:05:51] Filtering fragments with small insert size (remaining=6051989)
[2026-06-04T21:05:53] Filtering alignments with long gaps (remaining=6051989)
[2026-06-04T21:05:55] Filtering fragments with both mates in the same gene (remaining=6050783)
[2026-06-04T21:05:58] Filtering fusions arising from hairpin structures (remaining=5762561)
[2026-06-04T21:06:00] Filtering reads with a mismatch p-value <=0.01 (remaining=2864324)
[2026-06-04T21:06:15] Filtering reads with low entropy (k-mer content >=60%) (remaining=1254746)
[2026-06-04T21:06:27] Finding fusions and counting supporting reads (total=937452)
[2026-06-04T21:06:41] Merging adjacent fusion breakpoints (remaining=929219)
[2026-06-04T21:06:43] Filtering multi-mapping fusions by alignment score and read support (remaining=551699)
[2026-06-04T21:07:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:07:21] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=550565)
[2026-06-04T21:07:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=357427)
[2026-06-04T21:07:23] Filtering fusions with <2 supporting reads (remaining=35743)
[2026-06-04T21:07:24] Filtering fusions with an e-value >=0.3 (remaining=7456)
[2026-06-04T21:07:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7486)
[2026-06-04T21:07:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7400)
[2026-06-04T21:07:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7402)
[2026-06-04T21:07:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7276)
[2026-06-04T21:07:37] Searching for fusions with spliced split reads (remaining=7371)
[2026-06-04T21:07:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=4713)
[2026-06-04T21:07:44] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4670)
[2026-06-04T21:07:45] Searching for fusions with >=4 spliced events (remaining=5508)
[2026-06-04T21:07:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2072)
[2026-06-04T21:07:59] Filtering fusions with anchors <=23nt (remaining=1618)
[2026-06-04T21:08:00] Filtering end-to-end fusions with low support (remaining=1572)
[2026-06-04T21:08:00] Filtering fusions with no coverage around the breakpoints (remaining=1540)
[2026-06-04T21:08:01] Indexing gene sequences 
[2026-06-04T21:08:08] Filtering genes with >=30% identity (remaining=471)
[2026-06-04T21:08:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=162)
[2026-06-04T21:08:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=151)
[2026-06-04T21:08:16] Searching for additional isoforms (remaining=185)
[2026-06-04T21:08:17] Assigning confidence scores to events 
[2026-06-04T21:08:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:08:21] Writing fusions to file '659_Lx-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:08:23] Writing discarded fusions to file '659_Lx-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:08:51] Freeing resources
[2026-06-04T21:09:09] Done (elapsed time=00:10:37, CPU time=00:10:36, peak memory=15.7gb)