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Old 05-18-2009, 03:08 PM   #1
joseph
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Location: ca

Join Date: Feb 2008
Posts: 39
Default 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 ....
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