[2026-05-28T00:03:48] Launching Arriba 2.4.0
[2026-05-28T00:03:48] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:03:56] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:04:01] Reading chimeric alignments from '659_cIX-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3165233)
[2026-05-28T00:06:21] Marking multi-mapping alignments (marked=1989962)
[2026-05-28T00:06:22] Detecting strandedness (reverse)
[2026-05-28T00:06:22] Assigning strands to alignments 
[2026-05-28T00:06:23] Annotating alignments 
[2026-05-28T00:06:36] Filtering duplicates (remaining=1795134)
[2026-05-28T00:06:38] 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=1699959)
[2026-05-28T00:06:39] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1699959)
[2026-05-28T00:06:40] Filtering viral contigs with expression lower than the top 5 (remaining=1699959)
[2026-05-28T00:06:41] Filtering viral contigs with less than 5% coverage (remaining=1699959)
[2026-05-28T00:06:43] Estimating fragment length (mate gap mean=-87.6936, mate gap stddev=28.6824, read length mean=132.688)
[2026-05-28T00:06:43] Filtering read-through fragments with a distance <=10000bp (remaining=1599750)
[2026-05-28T00:06:44] Filtering inconsistently clipped mates (remaining=1567258)
[2026-05-28T00:06:44] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1515914)
[2026-05-28T00:06:46] Filtering fragments with small insert size (remaining=1515673)
[2026-05-28T00:06:46] Filtering alignments with long gaps (remaining=1515673)
[2026-05-28T00:06:47] Filtering fragments with both mates in the same gene (remaining=1515372)
[2026-05-28T00:06:48] Filtering fusions arising from hairpin structures (remaining=1412215)
[2026-05-28T00:06:49] Filtering reads with a mismatch p-value <=0.01 (remaining=620437)
[2026-05-28T00:06:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=263986)
[2026-05-28T00:06:56] Finding fusions and counting supporting reads (total=225030)
[2026-05-28T00:07:03] Merging adjacent fusion breakpoints (remaining=223554)
[2026-05-28T00:07:03] Filtering multi-mapping fusions by alignment score and read support (remaining=144617)
[2026-05-28T00:07:16] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:07:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=143646)
[2026-05-28T00:07:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=72983)
[2026-05-28T00:07:19] Filtering fusions with <2 supporting reads (remaining=9739)
[2026-05-28T00:07:19] Filtering fusions with an e-value >=0.3 (remaining=2940)
[2026-05-28T00:07:19] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2973)
[2026-05-28T00:07:20] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2947)
[2026-05-28T00:07:21] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2947)
[2026-05-28T00:07:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2370)
[2026-05-28T00:07:23] Searching for fusions with spliced split reads (remaining=2408)
[2026-05-28T00:07:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=1803)
[2026-05-28T00:07:25] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1790)
[2026-05-28T00:07:25] Searching for fusions with >=4 spliced events (remaining=1963)
[2026-05-28T00:07:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=587)
[2026-05-28T00:07:38] Filtering fusions with anchors <=23nt (remaining=486)
[2026-05-28T00:07:38] Filtering end-to-end fusions with low support (remaining=472)
[2026-05-28T00:07:38] Filtering fusions with no coverage around the breakpoints (remaining=450)
[2026-05-28T00:07:39] Indexing gene sequences 
[2026-05-28T00:07:42] Filtering genes with >=30% identity (remaining=197)
[2026-05-28T00:07:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=135)
[2026-05-28T00:07:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=114)
[2026-05-28T00:07:47] Searching for additional isoforms (remaining=135)
[2026-05-28T00:07:48] Assigning confidence scores to events 
[2026-05-28T00:07:49] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:07:49] Writing fusions to file '659_cIX-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:07:50] Writing discarded fusions to file '659_cIX-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:08:01] Freeing resources
[2026-05-28T00:08:07] Done (elapsed time=00:04:19, CPU time=00:04:18, peak memory=7.46gb)