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  • Myrna error

    Dear All,

    Myrna software: http://bowtie-bio.sourceforge.net/myrna/index.shtml
    I am trying to use Myrna software to analyze RNA-seq data from two cell-lines. We repeated experiments twice for each of the cell line hence I merged the data from repeated experiments. However, I am getting an error message while using following command:
    myrna_local --input=Cell1_ Cell2.manifest --preprocess --reference=MYRNA_REFS/human_ensembl_58 --output=output_full --cpus=8 --intermediate=~/intermediate --keep-all --quality=phred64 --family=poisson --tempdir=~/temp

    I am getting following error message:
    Normalization: lup
    Output URL: /gs1/users/rakesh/CIT/Analysis/Myrna/intermediate/count
    Processing label Normal-Subject1-Lane1/2
    stat /gs1/users/rakesh/CIT/Analysis/Myrna/intermediate/count/Normal-Subject1-Lane1/2.txt >& /dev/null
    stat /gs1/users/rakesh/CIT/Analysis/Myrna/intermediate/count/Normal-Subject1-Lane1/2.norm >& /dev/null
    stat /gs1/users/rakesh/CIT/Analysis/Myrna/intermediate/count/Normal-Subject1-Lane1/2.norms >& /dev/null
    mv: cannot move `.tmp.Normal.pl.29153' to `Normal-Subject1-Lane1/2.txt': No such file or directory
    stat /gs1/users/rakesh/CIT/Analysis/Myrna/intermediate/count/2.txt >& /dev/null
    cp Normal-Subject1-Lane1/2.txt /gs1/users/rakesh/CIT/Analysis/Myrna/intermediate/count/ >&2
    cp: cannot stat `Normal-Subject1-Lane1/2.txt': No such file or directory
    Can't load Normal-Subject1-Lane1/2.txt to /gs1/users/rakesh/CIT/Analysis/Myrna/intermediate/count/ (256)

    The Cell1_ Cell2.manifest file details are:
    /data/rakesh/CIT/Analysis/Myrna/Cell1_F_combined.txt 0 /data/rakesh/CIT/Analysis/Myrna/Cell1_R_combined.txt 0 Normal-Subject1-Lane1
    /data/rakesh/CIT/Analysis/Myrna/Cell2_F_combined.txt 0 /data/rakesh/CIT/Analysis/Myrna/Cell2_R_combined.txt 0 Tumor-Subject1-Lane1

    Can you please help me to solve the issue?

    I really appreciate your help,

    Thanks,

    Rakesh

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