Question: AddOrReplaceReadGroups error -
1
gravatar for phylofun
5 weeks ago by
phylofun10
phylofun10 wrote:

I want to do a for loop around the picard tool, AddOrReplaceReadGroups, but I get an error that has something to do with my input and output paths (I think). Can someone tell me where I went wrong with this:

# pwd: /Users/phylofun/Downloads/project

for i in mapping/*-pe.bam;
do
    java -jar ~/miniconda2/jar/AddOrReplaceReadGroups.jar \
    I="$i" \
    SORT_ORDER=coordinate \
    RGPL=illumina \
    RGPU=D109LACXX \
    RGLB=Lib1 \
    RGID="${i%-pe.bam}" \
    RGSM="${i%-pe.bam}" \
    VALIDATION_STRINGENCY=LENIENT \
    O=picard/"${i%-pe.bam}-pe-RG.bam"
done

error: Cannot write file: /Users/phylofun/Downloads/project/picard/mapping/sample1-pe-RG.bam. Neither file nor parent directory exist.
picard • 127 views
ADD COMMENTlink modified 5 weeks ago by RamRS20k • written 5 weeks ago by phylofun10
2
gravatar for austinjpaul
5 weeks ago by
austinjpaul20
austinjpaul20 wrote:

Your input files are coming from the ./mapping/ directory.

Your output path is specified as ./picard/mapping/ directory. However, files can't be written there if that folder doesn't exist.

Try running mkdir ./picard/mapping and then running the script again. Or change your output file names to not be nested under ./picard so that they use the existing ./mapping folder.

Hope that helps!

ADD COMMENTlink modified 5 weeks ago by RamRS20k • written 5 weeks ago by austinjpaul20

Welcome to Biostars and thank you for the contribution! Please use the formatting bar (especially the code option) to present your post better. You can use backticks (`text` becomes text) for inline code, or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
code_formatting

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by RamRS20k
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