[2026-06-08T07:46:01] Launching Arriba 2.4.0
[2026-06-08T07:46:01] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:46:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:46:24] Reading chimeric alignments from '1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=4574580)
[2026-06-08T07:49:59] Marking multi-mapping alignments (marked=3061122)
[2026-06-08T07:50:01] Detecting strandedness (reverse)
[2026-06-08T07:50:01] Assigning strands to alignments 
[2026-06-08T07:50:02] Annotating alignments 
[2026-06-08T07:50:20] Filtering duplicates (remaining=3691894)
[2026-06-08T07:50:25] 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=3410126)
[2026-06-08T07:50:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3410126)
[2026-06-08T07:50:27] Filtering viral contigs with expression lower than the top 5 (remaining=3410126)
[2026-06-08T07:50:29] Filtering viral contigs with less than 5% coverage (remaining=3410126)
[2026-06-08T07:50:31] Estimating fragment length (mate gap mean=-79.925, mate gap stddev=26.4746, read length mean=118.561)
[2026-06-08T07:50:31] Filtering read-through fragments with a distance <=10000bp (remaining=3302667)
[2026-06-08T07:50:32] Filtering inconsistently clipped mates (remaining=3259453)
[2026-06-08T07:50:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3194047)
[2026-06-08T07:50:35] Filtering fragments with small insert size (remaining=3193674)
[2026-06-08T07:50:36] Filtering alignments with long gaps (remaining=3193674)
[2026-06-08T07:50:37] Filtering fragments with both mates in the same gene (remaining=3193113)
[2026-06-08T07:50:38] Filtering fusions arising from hairpin structures (remaining=3088161)
[2026-06-08T07:50:39] Filtering reads with a mismatch p-value <=0.01 (remaining=1521045)
[2026-06-08T07:50:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=673646)
[2026-06-08T07:50:55] Finding fusions and counting supporting reads (total=645301)
[2026-06-08T07:51:06] Merging adjacent fusion breakpoints (remaining=643017)
[2026-06-08T07:51:07] Filtering multi-mapping fusions by alignment score and read support (remaining=371397)
[2026-06-08T07:51:25] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:51:30] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=370909)
[2026-06-08T07:51:31] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=325456)
[2026-06-08T07:51:32] Filtering fusions with <2 supporting reads (remaining=10024)
[2026-06-08T07:51:32] Filtering fusions with an e-value >=0.3 (remaining=1922)
[2026-06-08T07:51:32] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1966)
[2026-06-08T07:51:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1945)
[2026-06-08T07:51:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1945)
[2026-06-08T07:51:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1945)
[2026-06-08T07:51:39] Searching for fusions with spliced split reads (remaining=1989)
[2026-06-08T07:51:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=1529)
[2026-06-08T07:51:44] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1499)
[2026-06-08T07:51:44] Searching for fusions with >=4 spliced events (remaining=1648)
[2026-06-08T07:51:45] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=556)
[2026-06-08T07:52:04] Filtering fusions with anchors <=23nt (remaining=440)
[2026-06-08T07:52:04] Filtering end-to-end fusions with low support (remaining=429)
[2026-06-08T07:52:05] Filtering fusions with no coverage around the breakpoints (remaining=419)
[2026-06-08T07:52:05] Indexing gene sequences 
[2026-06-08T07:52:09] Filtering genes with >=30% identity (remaining=184)
[2026-06-08T07:52:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=130)
[2026-06-08T07:52:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=130)
[2026-06-08T07:52:13] Searching for additional isoforms (remaining=154)
[2026-06-08T07:52:14] Assigning confidence scores to events 
[2026-06-08T07:52:17] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:52:17] Writing fusions to file '1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:52:18] Writing discarded fusions to file '1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:52:43] Freeing resources
[2026-06-08T07:52:54] Done (elapsed time=00:06:53, CPU time=00:06:53, peak memory=8.95gb)