BrendaLee1

Hi! Firstly Thank you for your reply, I tyied your new version, but still cannot work on Pacbio sequence data. Information as blow: I tested advntr by one chromosome's Pacbio...

**Hi Tony, I tried both danbing-tk-1.3.2 and danbing-tk-1.0, I find that danbing-tk-1.0 can run successfully 'snakemake -p -s ../pipeline/GoodPanGenomeGraph.snakefile -j 4 --rerun-incomplete --output-wait 3', but danbing-tk-1.3.2 always have the following...

Hi, Thanks for your reply, but the error message still occur: Error in rule GenRawGenomeGraph: jobid: 11 output: /rd1/laixh/soft/danbing-tk-1.3.2/test/output/HG00733.rawPB.tr.kmers, /rd1/laixh/soft/danbing-tk-1.3.2/test/output/HG00733.rawPB.ntr.kmers, /rd1/laixh/soft/danbing-tk-1.3.2/test/output/HG00733.rawPB.graph.kmers shell: set -eu ulimit -c 20000 cd /rd1/laixh/soft/danbing-tk-1.3.2/test/output/ type...

Hi, I tried the repeat definition format as you suggested, but got the error below: Locus Processing: Error at BED line 60365: STRUC field missing, version 1.4.1. I want to...

Hi, Thank you for your advice, it works.

Hi, Thank you for your reply, The bcftools I use is 1.17. I changed the command line: bcftools mpileup -f hg38.fa --threads 15 -o ../SNP/$nvcf -O v $file bcftools call...

Hi, I restart bcftools with different RAM, I find that incomplete output files were due to small RAM, after I enlarge the RAM (~150G) the output can be finished properly.

I call SNPs for PacBio HiFi assembled contigs of human (~3G). I try to call SNPs for drosophila assembled contig recently, but similar error occured, the vcf file was trucated...

Hi, I call SNP for 145 PacBio HiFi assembled human genomes using the following command: bcftools mpileup -Ou -f hg38.fa -b BamList.txt -r chr1:1-2000000 | bcftools call -cv --ploidy 1...