Question: dwgsim_eval: read not generated by dwgsim?
0
gravatar for fiona.newberry
2.3 years ago by
fiona.newberry80 wrote:

I am trying to evaluate mapping accuracy of BWA (by using false positive and true positive).

I want to use dwgsim_eval to get this information from my files. Here is the link to the manual: https://github.com/nh13/DWGSIM/wiki/Evaluating-Mappings-from-DWGSIM

It states if the alignments were made from BWA to use "-b", which I am using but I am getting an error message.

Here is my code:

dwgsim_eval -b sorted_sub_human_BWA.bam

And here is the error message:

0************************************************************
In function "process_bam": Fatal Error[OutOfRange]. Variable/Value: simulated.7796575.
Message: [dwgsim_eval] read was not generated by dwgsim?.
 ***** Exiting due to errors *****
************************************************************

Not sure if there is maybe something wrong with my files? Any help would be greatly appreciated.

dwgsim_eval • 543 views
ADD COMMENTlink written 2.3 years ago by fiona.newberry80

how did you generate sorted_sub_human_BWA.bam ?

ADD REPLYlink written 2.3 years ago by Pierre Lindenbaum123k

Using this code:

for filename in ./seqtk_2/subsample_1/*_1.fq.gz;
do file=`echo $filename|sed 's/_1.fq.gz//'`;
filenopath=`basename $file`;
outputpath=./BWA/seqtk_2/subsample_1;
bwa mem -v 3 ./combine_reference.fa.gz ${file}_1.fq.gz ${file}_2.fq.gz | sambamba view -S -f bam /dev/stdin | sambamba sort /dev/stdin -o ${outputpath}/sorted_${filenopath}_BWA.bam;
done
ADD REPLYlink written 2.3 years ago by fiona.newberry80
0
gravatar for Pierre Lindenbaum
2.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

how did you generate /seqtk_2/subsample_1/*_1.fq.gz ?

(reads must be generated by dwgsim.... )

This utility evaluates the mappings from reads produced by dwgsim

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Pierre Lindenbaum123k

I used a simulator called Mason. I see the problem now. I was assuming it meant reads could be simulated by any program but have to specify if it generated by BWA. Are there any other programs that I can use to determine false positive and true positive rate? I want to make roc curves for several different aligners I am trying

ADD REPLYlink written 2.3 years ago by fiona.newberry80

why don't you just use the fastq generated by dwgsim ?

ADD REPLYlink written 2.3 years ago by Pierre Lindenbaum123k

I selected the simulator based on the features. I am building an artificial gut community model (with 1000's of sequences) and dwgsim did not have some of the features I needed

ADD REPLYlink written 2.3 years ago by fiona.newberry80
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