[2026-05-28T00:02:41] Launching Arriba 2.4.0
[2026-05-28T00:02:41] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:02:50] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:02:54] Reading chimeric alignments from '659_cRB-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3827688)
[2026-05-28T00:05:06] Marking multi-mapping alignments (marked=2442178)
[2026-05-28T00:05:08] Detecting strandedness (reverse)
[2026-05-28T00:05:08] Assigning strands to alignments 
[2026-05-28T00:05:09] Annotating alignments 
[2026-05-28T00:05:23] Filtering duplicates (remaining=1653783)
[2026-05-28T00:05:26] 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=1560214)
[2026-05-28T00:05:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1560214)
[2026-05-28T00:05:27] Filtering viral contigs with expression lower than the top 5 (remaining=1560214)
[2026-05-28T00:05:29] Filtering viral contigs with less than 5% coverage (remaining=1560214)
[2026-05-28T00:05:30] Estimating fragment length (mate gap mean=-85.0804, mate gap stddev=27.0625, read length mean=121.901)
[2026-05-28T00:05:30] Filtering read-through fragments with a distance <=10000bp (remaining=1445568)
[2026-05-28T00:05:31] Filtering inconsistently clipped mates (remaining=1414702)
[2026-05-28T00:05:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1365597)
[2026-05-28T00:05:33] Filtering fragments with small insert size (remaining=1365181)
[2026-05-28T00:05:34] Filtering alignments with long gaps (remaining=1365181)
[2026-05-28T00:05:34] Filtering fragments with both mates in the same gene (remaining=1364940)
[2026-05-28T00:05:35] Filtering fusions arising from hairpin structures (remaining=1287401)
[2026-05-28T00:05:36] Filtering reads with a mismatch p-value <=0.01 (remaining=500389)
[2026-05-28T00:05:40] Filtering reads with low entropy (k-mer content >=60%) (remaining=245958)
[2026-05-28T00:05:43] Finding fusions and counting supporting reads (total=223055)
[2026-05-28T00:05:50] Merging adjacent fusion breakpoints (remaining=220679)
[2026-05-28T00:05:50] Filtering multi-mapping fusions by alignment score and read support (remaining=130325)
[2026-05-28T00:06:07] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:06:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=129806)
[2026-05-28T00:06:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=68624)
[2026-05-28T00:06:10] Filtering fusions with <2 supporting reads (remaining=6989)
[2026-05-28T00:06:10] Filtering fusions with an e-value >=0.3 (remaining=1672)
[2026-05-28T00:06:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1707)
[2026-05-28T00:06:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1681)
[2026-05-28T00:06:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1681)
[2026-05-28T00:06:12] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1644)
[2026-05-28T00:06:14] Searching for fusions with spliced split reads (remaining=1714)
[2026-05-28T00:06:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=1324)
[2026-05-28T00:06:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1310)
[2026-05-28T00:06:17] Searching for fusions with >=4 spliced events (remaining=1405)
[2026-05-28T00:06:18] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=396)
[2026-05-28T00:06:29] Filtering fusions with anchors <=23nt (remaining=329)
[2026-05-28T00:06:30] Filtering end-to-end fusions with low support (remaining=324)
[2026-05-28T00:06:30] Filtering fusions with no coverage around the breakpoints (remaining=317)
[2026-05-28T00:06:30] Indexing gene sequences 
[2026-05-28T00:06:32] Filtering genes with >=30% identity (remaining=121)
[2026-05-28T00:06:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=51)
[2026-05-28T00:06:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=51)
[2026-05-28T00:06:34] Searching for additional isoforms (remaining=59)
[2026-05-28T00:06:34] Assigning confidence scores to events 
[2026-05-28T00:06:35] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:06:36] Writing fusions to file '659_cRB-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:06:36] Writing discarded fusions to file '659_cRB-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:06:47] Freeing resources
[2026-05-28T00:06:56] Done (elapsed time=00:04:15, CPU time=00:04:14, peak memory=8.11gb)