Error: failed to locate the BWA index.

Question

[L_LANKA]

Hello!

Today I had attempts to write code for automation my pipeline. I tried make It in Jupyter but some packages, for example os.startfile (path[, operation]), not intended for Unix sistem. Now I attempt make it in R-studio and I have some questions:

1) How I should run program? For example, I had attempts run bwa mem and I have problem. I wrote in terminal:

bwa.path <- "/home/valera/Utilits/bwa-0.7.16a/bwakit/"
system(paste(bwa.path, "run-bwamem -M /home/valera/bam/GRCh38_latest_genomic.fna /home/valera/bam/Rep2.fastq.gz>/home/valera/bam/Prob_obr.sam","index", sep=""))

and the program makes output ERROR: failed to locate the BWA index.

2) Second question from first, what I should indicate in "index"?

3) Is It good idea write automatically pipeline on R-language?

[lieven.sterck]

Hello L_LANKA,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

Answer 1

[JC]

The system in R is creating a command like the one you type in your terminal, the index is the location of the index base name, the intriguing part in the "run-bwamem", that looks like is a script or wrapper. If you are just running BWA mem, the minimal command will be:

bwa.path <- "/home/valera/Utilits/bwa-0.7.16a/bwa"
index.path <- "/home/valera/bam/GRCh38_latest_genomic"
system(paste(bwa.path, "-M", index.path, "/home/valera/bam/Rep2.fastq.gz", ">", "/home/valera/bam/Prob_obr.sam", sep=" "))

for the last question, it is not impossible to have a pipeline in R, but maybe Bash or other workflow managers (SnakeMake, NextFlow) are better for this.

[L_LANKA]

Thank you so mush! I tried use it now. I have error:

/home/valera/Utilits/bwa-0.7.16a/bwa: not found

and

Предупреждение:
В system(paste(bwa.path, "-M", index.path, "/home/valera/bam/Rep2.fastq.gz",  :
  ошибка запуска команды

[JC]

where is installed BWA? /usr/local/bin/bwa?

[L_LANKA]

Yes! When I used it in terminal, i wrote:

cd ~/Utilits/bwa-0.7.16a/bwakit
bwa

It`s work normal.

[JC]

the your code should be:

bwa.path <- "/home/valera/Utilits/bwa-0.7.16a/bwakit/bwa"

Also check your index, where did you run "bwa index"? You should see some file with extension ".rpac, .amb, .ann, .pac, .bwt, .rbwt, .rsa, .sa"

[L_LANKA]

I don't understand what is wrong. I make index by:

bwa.path <- "/home/valera/Utilits/bwa-0.7.16a/bwa"
system("bwa index -a bwtsw /home/valera/bam/GRCh38_alignment.fa")

and It works good!!! When It finished worked (It made index), I ran script for sam. It prints again message about error. I had attempts change script :

system(paste(bwa.path, "-M", index.path, " /home/valera/bam/Rep2.fastq.gz > /home/valera/bam/Prob_obr.sam"

I have old error. It's so sad :(

[L_LANKA]

I decided this problem. When I wrote in script:

system("bwa mem /home/valera/bam/GRCh38_alignment.fa /home/valera/bam/Rep2.fastq.gz > /home/valera/bam/Prob_obr.sam")

It`s work normal.