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  • joseph
    Member
    • Feb 2008
    • 39
    #1

    ERANGE: runRNAPairedAnalysis.sh with error at the rnafarPairs.py step

    Hi
    I am analyzing one PE lane with files ‘s_3_1_sequence.txt’ and ‘s_3_2_sequence.txt’, which I mapped with Bowtie and then used to create s3.rds.
    I got the error below when I run runRNAPairedAnalysis.sh
    Thanks for the help
    Joseph


    .....
    /proj/genome/commoncode/rnafarPairs.py: version 3.5
    caching ....
    dataset s3.rds
    metadata:
    bowtie_mapped True
    dataType RNA
    paired True
    rdsVersion 1.1
    readsize 34
    user J.Dhahbi
    7118451 unique reads, 590197 spliced reads and 3588212 multireads
    default cache size is 1000000 pages
    found index
    chr1
    Traceback (most recent call last):
    File "/proj/genome/commoncode/rnafarPairs.py", line 78, in <module>
    uniqDict = RDS.getReadsDict(fullChrom=True, chrom=achrom, noSense=True, withFlag=True, withPairID=True, doUniqs=True, readIDDict=True)
    File "/proj/genome/commoncode/commoncode.py", line 1021, in getReadsDict
    (theReadID, pairID) = readID.split('/')
    ValueError: unpack list of wrong size
    /proj/genome/commoncode/normalizeExpandedExonic.py: version 5.4
    human cached
    caching ....
    Tags: None
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