Greg

Hi, Yes, though dependent on the nature(read length/quality) and quantity of your input data, seeing a decrease in N50 from raw reads to corrected preads is typical, especially in a...

Hi, You have sufficient raw coverage (almost 90-fold) so there should be plenty of raw data to get a decent draft assembly. What I see from your pre-asesmbled statistics, however...

I agree pread correction doesn't appear to be proceeding as efficiently as it should be, which is still what's limiting the assembly. However, I also notice in your latest assembly...

I also just ran into this issue. pipeline works fine w/ hg38, but if I switch to chm13v2 I get no reads mapped. I thought I was going nuts, reassuring...

Hi Luca, The settings you have listed seem reasonable given the coverage and expected genome size you have. The only things I might recommend would be: 1) in pa_HPCdaligner_option &...

FYI - I had this same error and it was caused by having improper character in my sample names. In my case it was a `#` sign. Solved the problem...

On Catalina I had this same issue. The solution is probably a little late for you, but for people in the future, the way I solved it was by installing...

Hi Dario, It’s typical that there are fewer contigs present after running the unzip pipeline. This most often occurs in coverage limited situations. e.g. you might have a primary contig...

The haplotigs associated with each primary contig represent a mixture of the two haplotypes, and are not phased relative to each other. The haplotigs are basically structural variation that was...

Hi @wsuplantpathology Can you post the contents of: `/data/chen/PacBio/PST/assembly/falcon/raw_all/3-unzip/reads/task.json ` It looks like the task finished successfully. Does `3-unzip/reads/track_reads_done` exist, and is `3-unzip/reads/ctg_list` non-empty? If so, you may be able...