A 10% dDocent Run

A bit optimistic here but I thought I’d run an assembly with 10% of the data from each individual and see how many configs I could produce. It did run and produced 394,146 contigs from 969,927 sequences. But unfortunately, it was running on all the data to map at 10% and was going to take just too long.


January 27, 2023

So this time I made a small representation of the overall sequences, using: - 10% of each individual - Renamed to not have period in population name for each state (thinking that may be why I’ve had failures in the past). - Saved to different folder.


files <- list.files("all",pattern="F.fq.gz")
for( i in 1:length(files) ) {
    file <- files[i]
    tmp <- strsplit(file, split="\\.")[[1]]
    ofile <- paste( paste( tmp[1],
                        tmp[3], tmp[4], tmp[5], sep=".")
    cmd <- paste("seqtk sample ./all/",
                     " 0.10 | gzip > ./all010/", 
    cat( format(i/length(files), digits=3), " ", ofile, "\n")

It ran for a while, then died. So I tried it again and there were some issues with dDocent not recognizing the the files as being gz files… So I had to unzip all the 10% individuals and redo them.

Finally it went through but I got a few errors along the way.

Trimming reads and simultaneously assembling reference sequences

Removing the _1 character and replacing with /1 in the name of every sequence
parallel: Warning: Starting 16 processes took > 2 sec.
parallel: Warning: Consider adjusting -j. Press CTRL-C to stop.

Then it gave me the prompt for number of unique sequences per individual.

Please choose data cutoff. In essence, you are picking a minimum (within individual) coverage level for a read (allele) to be used in the reference assembly.

I had hit the return button a few times and it ran using some ‘default’ value.

This time it did finish and made contigs.

At this point, all configuration information has been entered and dDocent may take several hours to run.

It is recommended that you move this script to a background operation and disable terminal input and output.

All data and logfiles will still be recorded.
To do this:
Press **control** and **Z** simultaneously
Type **bg** and press enter
Type **disown -h** and press enter
Now sit back, relax, and wait for your analysis to finish

dDocent assembled 969927 sequences (after cutoffs) into 394146 contigs
Using BWA to map reads

So at this point, I let it run for a while longer and then realized I was not going to use the 10% representation and would be using another assembly. So I killed the mapping.