[2026-06-08T08:41:33] Launching Arriba 2.4.0
[2026-06-08T08:41:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:41:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:41:49] Reading chimeric alignments from '1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=14726969)
[2026-06-08T08:49:31] Marking multi-mapping alignments (marked=9524788)
[2026-06-08T08:49:36] Detecting strandedness (reverse)
[2026-06-08T08:49:36] Assigning strands to alignments 
[2026-06-08T08:49:39] Annotating alignments 
[2026-06-08T08:50:21] Filtering duplicates (remaining=10777239)
[2026-06-08T08:50:31] 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=10126360)
[2026-06-08T08:50:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=10126360)
[2026-06-08T08:50:36] Filtering viral contigs with expression lower than the top 5 (remaining=10126360)
[2026-06-08T08:50:42] Filtering viral contigs with less than 5% coverage (remaining=10126360)
[2026-06-08T08:50:44] Estimating fragment length (mate gap mean=-84.078, mate gap stddev=28.2812, read length mean=128.873)
[2026-06-08T08:50:45] Filtering read-through fragments with a distance <=10000bp (remaining=9757052)
[2026-06-08T08:50:47] Filtering inconsistently clipped mates (remaining=9597892)
[2026-06-08T08:50:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9422945)
[2026-06-08T08:50:56] Filtering fragments with small insert size (remaining=9421771)
[2026-06-08T08:50:58] Filtering alignments with long gaps (remaining=9421771)
[2026-06-08T08:51:01] Filtering fragments with both mates in the same gene (remaining=9420554)
[2026-06-08T08:51:04] Filtering fusions arising from hairpin structures (remaining=8996929)
[2026-06-08T08:51:07] Filtering reads with a mismatch p-value <=0.01 (remaining=4585331)
[2026-06-08T08:51:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=2236998)
[2026-06-08T08:51:43] Finding fusions and counting supporting reads (total=2038531)
[2026-06-08T08:52:08] Merging adjacent fusion breakpoints (remaining=2029089)
[2026-06-08T08:52:11] Filtering multi-mapping fusions by alignment score and read support (remaining=1204736)
[2026-06-08T08:52:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:53:06] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1203430)
[2026-06-08T08:53:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1021497)
[2026-06-08T08:53:09] Filtering fusions with <2 supporting reads (remaining=39112)
[2026-06-08T08:53:10] Filtering fusions with an e-value >=0.3 (remaining=6010)
[2026-06-08T08:53:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6102)
[2026-06-08T08:53:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6012)
[2026-06-08T08:53:18] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6012)
[2026-06-08T08:53:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5884)
[2026-06-08T08:53:28] Searching for fusions with spliced split reads (remaining=5926)
[2026-06-08T08:53:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=4111)
[2026-06-08T08:53:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4072)
[2026-06-08T08:53:39] Searching for fusions with >=4 spliced events (remaining=5157)
[2026-06-08T08:53:42] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2176)
[2026-06-08T08:54:07] Filtering fusions with anchors <=23nt (remaining=1677)
[2026-06-08T08:54:08] Filtering end-to-end fusions with low support (remaining=1639)
[2026-06-08T08:54:10] Filtering fusions with no coverage around the breakpoints (remaining=1592)
[2026-06-08T08:54:11] Indexing gene sequences 
[2026-06-08T08:54:19] Filtering genes with >=30% identity (remaining=424)
[2026-06-08T08:54:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=226)
[2026-06-08T08:54:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=179)
[2026-06-08T08:54:29] Searching for additional isoforms (remaining=239)
[2026-06-08T08:54:31] Assigning confidence scores to events 
[2026-06-08T08:54:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:54:38] Writing fusions to file '1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:54:42] Writing discarded fusions to file '1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:55:38] Freeing resources
[2026-06-08T08:56:01] Done (elapsed time=00:14:28, CPU time=00:14:27, peak memory=19.6gb)