[2026-05-27T23:56:41] Launching Arriba 2.4.0
[2026-05-27T23:56:41] Loading assembly from 'ref_genome.fa' 
[2026-05-27T23:56:51] Loading annotation from 'ref_annot.gtf' 
[2026-05-27T23:56:56] Reading chimeric alignments from '659_6i-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3887083)
[2026-05-27T23:59:04] Marking multi-mapping alignments (marked=2515369)
[2026-05-27T23:59:06] Detecting strandedness (reverse)
[2026-05-27T23:59:06] Assigning strands to alignments 
[2026-05-27T23:59:07] Annotating alignments 
[2026-05-27T23:59:22] Filtering duplicates (remaining=1318168)
[2026-05-27T23:59:24] 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=1251038)
[2026-05-27T23:59:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1251038)
[2026-05-27T23:59:26] Filtering viral contigs with expression lower than the top 5 (remaining=1251038)
[2026-05-27T23:59:27] Filtering viral contigs with less than 5% coverage (remaining=1251038)
[2026-05-27T23:59:29] Estimating fragment length (mate gap mean=-87.9241, mate gap stddev=26.65, read length mean=126.486)
[2026-05-27T23:59:29] Filtering read-through fragments with a distance <=10000bp (remaining=1177220)
[2026-05-27T23:59:29] Filtering inconsistently clipped mates (remaining=1150857)
[2026-05-27T23:59:30] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1095740)
[2026-05-27T23:59:32] Filtering fragments with small insert size (remaining=1095530)
[2026-05-27T23:59:32] Filtering alignments with long gaps (remaining=1095530)
[2026-05-27T23:59:33] Filtering fragments with both mates in the same gene (remaining=1095241)
[2026-05-27T23:59:34] Filtering fusions arising from hairpin structures (remaining=1033414)
[2026-05-27T23:59:35] Filtering reads with a mismatch p-value <=0.01 (remaining=407678)
[2026-05-27T23:59:38] Filtering reads with low entropy (k-mer content >=60%) (remaining=190683)
[2026-05-27T23:59:41] Finding fusions and counting supporting reads (total=177714)
[2026-05-27T23:59:47] Merging adjacent fusion breakpoints (remaining=176324)
[2026-05-27T23:59:48] Filtering multi-mapping fusions by alignment score and read support (remaining=95857)
[2026-05-28T00:00:07] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:00:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=95293)
[2026-05-28T00:00:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=53822)
[2026-05-28T00:00:10] Filtering fusions with <2 supporting reads (remaining=5125)
[2026-05-28T00:00:11] Filtering fusions with an e-value >=0.3 (remaining=1456)
[2026-05-28T00:00:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1481)
[2026-05-28T00:00:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1438)
[2026-05-28T00:00:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1438)
[2026-05-28T00:00:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1407)
[2026-05-28T00:00:16] Searching for fusions with spliced split reads (remaining=1487)
[2026-05-28T00:00:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=1181)
[2026-05-28T00:00:19] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1171)
[2026-05-28T00:00:20] Searching for fusions with >=4 spliced events (remaining=1227)
[2026-05-28T00:00:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=295)
[2026-05-28T00:00:42] Filtering fusions with anchors <=23nt (remaining=245)
[2026-05-28T00:00:42] Filtering end-to-end fusions with low support (remaining=236)
[2026-05-28T00:00:43] Filtering fusions with no coverage around the breakpoints (remaining=227)
[2026-05-28T00:00:43] Indexing gene sequences 
[2026-05-28T00:00:47] Filtering genes with >=30% identity (remaining=88)
[2026-05-28T00:00:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=52)
[2026-05-28T00:00:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=48)
[2026-05-28T00:00:49] Searching for additional isoforms (remaining=59)
[2026-05-28T00:00:49] Assigning confidence scores to events 
[2026-05-28T00:00:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:00:51] Writing fusions to file '659_6i-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:00:51] Writing discarded fusions to file '659_6i-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:01:05] Freeing resources
[2026-05-28T00:01:17] Done (elapsed time=00:04:36, CPU time=00:04:34, peak memory=8.12gb)