AddOrReplaceReadGroups error -

Question

[phylofun]

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.

Answer 1

[austinjpaul]

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!

[Ram]

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