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using GNU parallel for bwa mem and samtools

Hi all, My (paired-end) sequencing data is comprised of several samples:

fq/S01_R1_fq.gz
fq/S01_R2_fq.gz
fq/S02_R1_fq.gz
fq/S02_R2_fq.gz

I need to align the reads to reference genome and to convert the output to BAM format. I'd like to use parallel for that but I don't know how to do it. That's what I got for now:

parallel "bwa mem \
-t 10 \
-M hg1kv37.fa {1} {2} \
-v 1 -R "@RG\tID:{1}\tSM:{1}\tPL:ILLUMINA\tLB:{1}" \
| samtools view -Sb - > {=1 s:fq/:aln/:;s:R1_fq\.gz:alignment.bam:; =}" ::: fq/*R1.fq.gz ::: fq/*R2.fq.gz

I tried without quotes:

parallel: Warning: Input is read from the terminal. You either know what you
parallel: Warning: are doing (in which case: YOU ARE AWESOME!) or you forgot
parallel: Warning: ::: or :::: or -a or to pipe data into parallel. If so
parallel: Warning: consider going through the tutorial: man parallel_tutorial
parallel: Warning: Press CTRL-D to exit.

So I added quotes but now I keep getting the following error:

/usr/bin/sh: aln/S01_alignment.bam: No such file or directory
[E::bwa_set_rg] no ID within the read group line

I guess samtools is trying to find the output file for some reason. Any suggestions?

samtools bwa parallel
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updated by ole.tange ole.tange • written by little_more • little_more

With quotes, you have nested double quotes, so your shell is seeing this as one block:

"bwa mem \
-t 10 \
-M hg1kv37.fa {1} {2} \
-v 1 -R "

And this as another block:

" \
| samtools view -Sb - > {=1 s:fq/:aln/:;s:R1_fq\.gz:alignment.bam:; =}"

I would create a bash script which takes R1 and R2 as arguments, performs the file name manipulations, and then maps with bwa. You can then use this script with GNU Parallel.

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written by h.mon h.mon

thank you all for your answers! @h.mon, I tried various combinations of quotes, including combinations of different types of quotes but it didn't help. @finswimmer, thanks for the link, I'll check it :)

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written by little_more • little_more

1 answer

It makes it easier to read and to test if you create a function and call that.

You can then test your function on a single file set before handing it to GNU Parallel:

bwatosam() {
  id="$1"

  bwa mem -t 10 -M -R "@RG\tID:{}\tSM:{}\tPL:ILLUMINA\tLB:{}" hg1kv37.fa "$id"_R1.fq.gz "$id"_R2.fq.gz |
    samtools view -o "$id".bam
}
export -f bwatosam

# --plus enables {%...} to remove a substring    
ls *_R1.fq.gz |
  parallel --plus bwatosam {%_R1.fq.gz}

(Are you coming for the anniversary party or hosting your own? https://www.gnu.org/software/parallel/10-years-anniversary.html )

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written by ole.tange ole.tange

Thank you so much for your solution! it seems to be exactly what I need but I get an error saying: 

/usr/bin/sh: line 1: mem: command not found

I think it might be caused by the fact that I use a variable for calling bwa:

bwa=/work/gr-fe/lawless/tool/bwa-0.7.17/bwa

and then 

$bwa mem ...

Do you know how can I handle it?

I also tried adding alias to bwa to my ~/.bashrc file so now I can call bwa from the terminal. But if I try to call bwa from within the script I get the error: 

/usr/bin/sh: line 1: bwa: command not found

Any help appreciated!

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written by little_more • little_more

I seem to overcome the problem with bwa: I just added a path to ~/.bashrc file.

Now I have another issue:

[E::bwa_idx_load_from_disk] fail to locate the index files

although the dir contains index files. What should I do?

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written by little_more • little_more

Just put the path to your index file within the function

bwa mem -t 10 -M -R "@RG\tID:{}\tSM:{}\tPL:ILLUMINA\tLB:{}" path/to/hg19/
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written by brunobsouzaa brunobsouzaa

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