[2026-06-04T20:38:29] Launching Arriba 2.4.0
[2026-06-04T20:38:29] Loading assembly from 'ref_genome.fa' 
[2026-06-04T20:38:37] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T20:38:40] Reading chimeric alignments from '659_cGW-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=4899819)
[2026-06-04T20:40:48] Marking multi-mapping alignments (marked=3371988)
[2026-06-04T20:40:50] Detecting strandedness (reverse)
[2026-06-04T20:40:50] Assigning strands to alignments 
[2026-06-04T20:40:51] Annotating alignments 
[2026-06-04T20:41:04] Filtering duplicates (remaining=1414313)
[2026-06-04T20:41:06] 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=1175174)
[2026-06-04T20:41:07] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1175174)
[2026-06-04T20:41:08] Filtering viral contigs with expression lower than the top 5 (remaining=1175174)
[2026-06-04T20:41:09] Filtering viral contigs with less than 5% coverage (remaining=1175174)
[2026-06-04T20:41:11] Estimating fragment length (mate gap mean=-84.4229, mate gap stddev=28.9935, read length mean=124.79)
[2026-06-04T20:41:11] Filtering read-through fragments with a distance <=10000bp (remaining=1123989)
[2026-06-04T20:41:12] Filtering inconsistently clipped mates (remaining=1096024)
[2026-06-04T20:41:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1053514)
[2026-06-04T20:41:14] Filtering fragments with small insert size (remaining=1052936)
[2026-06-04T20:41:15] Filtering alignments with long gaps (remaining=1052936)
[2026-06-04T20:41:15] Filtering fragments with both mates in the same gene (remaining=1052615)
[2026-06-04T20:41:16] Filtering fusions arising from hairpin structures (remaining=992294)
[2026-06-04T20:41:17] Filtering reads with a mismatch p-value <=0.01 (remaining=419209)
[2026-06-04T20:41:20] Filtering reads with low entropy (k-mer content >=60%) (remaining=148469)
[2026-06-04T20:41:23] Finding fusions and counting supporting reads (total=124916)
[2026-06-04T20:41:28] Merging adjacent fusion breakpoints (remaining=124116)
[2026-06-04T20:41:28] Filtering multi-mapping fusions by alignment score and read support (remaining=66320)
[2026-06-04T20:41:39] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T20:41:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=65760)
[2026-06-04T20:41:41] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=35909)
[2026-06-04T20:41:41] Filtering fusions with <2 supporting reads (remaining=3248)
[2026-06-04T20:41:41] Filtering fusions with an e-value >=0.3 (remaining=831)
[2026-06-04T20:41:41] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=847)
[2026-06-04T20:41:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=799)
[2026-06-04T20:41:42] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=799)
[2026-06-04T20:41:42] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=779)
[2026-06-04T20:41:44] Searching for fusions with spliced split reads (remaining=829)
[2026-06-04T20:41:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=675)
[2026-06-04T20:41:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=669)
[2026-06-04T20:41:46] Searching for fusions with >=4 spliced events (remaining=701)
[2026-06-04T20:41:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=185)
[2026-06-04T20:41:57] Filtering fusions with anchors <=23nt (remaining=152)
[2026-06-04T20:41:57] Filtering end-to-end fusions with low support (remaining=149)
[2026-06-04T20:41:57] Filtering fusions with no coverage around the breakpoints (remaining=144)
[2026-06-04T20:41:57] Indexing gene sequences 
[2026-06-04T20:41:58] Filtering genes with >=30% identity (remaining=57)
[2026-06-04T20:41:59] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=22)
[2026-06-04T20:41:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=19)
[2026-06-04T20:41:59] Searching for additional isoforms (remaining=23)
[2026-06-04T20:42:00] Assigning confidence scores to events 
[2026-06-04T20:42:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T20:42:00] Writing fusions to file '659_cGW-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T20:42:00] Writing discarded fusions to file '659_cGW-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T20:42:06] Freeing resources
[2026-06-04T20:42:13] Done (elapsed time=00:03:44, CPU time=00:03:43, peak memory=9.12gb)