[2026-06-08T08:25:25] Launching Arriba 2.4.0
[2026-06-08T08:25:25] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:25:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:25:42] Reading chimeric alignments from '1173_HOB_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=14636356)
[2026-06-08T08:32:35] Marking multi-mapping alignments (marked=10211699)
[2026-06-08T08:32:41] Detecting strandedness (reverse)
[2026-06-08T08:32:41] Assigning strands to alignments 
[2026-06-08T08:32:44] Annotating alignments 
[2026-06-08T08:33:28] Filtering duplicates (remaining=9824777)
[2026-06-08T08:33:37] 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=8901458)
[2026-06-08T08:33:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8901458)
[2026-06-08T08:33:42] Filtering viral contigs with expression lower than the top 5 (remaining=8901458)
[2026-06-08T08:33:48] Filtering viral contigs with less than 5% coverage (remaining=8901458)
[2026-06-08T08:33:51] Estimating fragment length (mate gap mean=-80.752, mate gap stddev=27.1241, read length mean=122.288)
[2026-06-08T08:33:51] Filtering read-through fragments with a distance <=10000bp (remaining=8526794)
[2026-06-08T08:33:54] Filtering inconsistently clipped mates (remaining=8361964)
[2026-06-08T08:33:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=8217558)
[2026-06-08T08:34:02] Filtering fragments with small insert size (remaining=8215990)
[2026-06-08T08:34:05] Filtering alignments with long gaps (remaining=8215990)
[2026-06-08T08:34:08] Filtering fragments with both mates in the same gene (remaining=8214664)
[2026-06-08T08:34:11] Filtering fusions arising from hairpin structures (remaining=7780196)
[2026-06-08T08:34:14] Filtering reads with a mismatch p-value <=0.01 (remaining=3673439)
[2026-06-08T08:34:31] Filtering reads with low entropy (k-mer content >=60%) (remaining=1688476)
[2026-06-08T08:34:48] Finding fusions and counting supporting reads (total=1523608)
[2026-06-08T08:35:13] Merging adjacent fusion breakpoints (remaining=1512863)
[2026-06-08T08:35:16] Filtering multi-mapping fusions by alignment score and read support (remaining=771624)
[2026-06-08T08:35:58] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:36:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=770338)
[2026-06-08T08:36:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=605150)
[2026-06-08T08:36:12] Filtering fusions with <2 supporting reads (remaining=25137)
[2026-06-08T08:36:13] Filtering fusions with an e-value >=0.3 (remaining=4071)
[2026-06-08T08:36:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4186)
[2026-06-08T08:36:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4138)
[2026-06-08T08:36:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4142)
[2026-06-08T08:36:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4069)
[2026-06-08T08:36:30] Searching for fusions with spliced split reads (remaining=4160)
[2026-06-08T08:36:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=2964)
[2026-06-08T08:36:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2949)
[2026-06-08T08:36:41] Searching for fusions with >=4 spliced events (remaining=3593)
[2026-06-08T08:36:43] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1588)
[2026-06-08T08:37:01] Filtering fusions with anchors <=23nt (remaining=1304)
[2026-06-08T08:37:02] Filtering end-to-end fusions with low support (remaining=1279)
[2026-06-08T08:37:03] Filtering fusions with no coverage around the breakpoints (remaining=1250)
[2026-06-08T08:37:04] Indexing gene sequences 
[2026-06-08T08:37:10] Filtering genes with >=30% identity (remaining=415)
[2026-06-08T08:37:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=174)
[2026-06-08T08:37:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=147)
[2026-06-08T08:37:17] Searching for additional isoforms (remaining=179)
[2026-06-08T08:37:19] Assigning confidence scores to events 
[2026-06-08T08:37:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:37:25] Writing fusions to file '1173_HOB_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:37:27] Writing discarded fusions to file '1173_HOB_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:38:21] Freeing resources
[2026-06-08T08:38:46] Done (elapsed time=00:13:21, CPU time=00:13:20, peak memory=19.3gb)