Error: read M00313:80:000000000-A4ALA:1:1101:16379:1657 has out of range quality values.

[GoogleCodeExporter]

What steps will reproduce the problem?

 Error: read M00313:80:000000000-A4ALA:1:1101:16379:1657 has out of range quality values.
Error: read M00313:80:000000000-A4ALA:1:1101:16379:1657 has out of range 
quality values.
Expected phred64.
Quality string: 
""###''##!##(($''('('())))())))'()'$))))())))((((&%)))(#()('(((((((((%&())''((&(
&'')))'))($&(''#'(&())(&')(( $((()))()#())#()')))('))%((())()&$)((((" 
'$'((((('''('(&% %%('(('''(('''!%''#'''''#" %''""%  !"'#''' "''#'%''#'
Check your data and re-run preprocess with the correct quality scaling flag.
[a5] Error preprocessing reads with SGA

What is the expected output? What do you see instead?

What version of the product are you using? On what operating system?

Please provide any additional information below.

Original issue reported on code.google.com by MAlab...@gmail.com on 30 Aug 2013 at 2:50

[GoogleCodeExporter]

i got the same error message mine looks like this
[a5] Begin: 17:32 on 8-3-2013
[a5] Found the following libraries:
     raw1:
      id=raw1
      p1=/Users/vengurlekarp/Desktop/k-10/Undetermined_S0_L001_R1_001.fastq
      p2=/Users/vengurlekarp/Desktop/k-10/Undetermined_S0_L001_R2_001.fastq
[a5] Found 1 libraries
[a5] Starting pipeline at step 1
[a5] Cleaning reads with SGA
[a5] Cleaning reads with SGA
preprocess: WARNING - it is suggested that the min read length is 40
preprocess: Using very short reads may considerably impact the performance
Parameters:
QualTrim: 10
QualFilter: at most 20 low quality bases
HardClip: 0
Min length: 29
Sample freq: 1
PE Mode: 0
Quality scaling: 3
MinGC: 0
MaxGC: 1
Outfile: stdout
Processing /Users/vengurlekarp/Desktop/k-10/Undetermined_S0_L001_R1_001.fastq

Error: read M01595:46:000000000-A4MWC:1:1101:14053:1410 has out of range 
quality values.
Expected phred64.
Quality string: "%!''('(#'#%#'"##'('"#'"#"##(#'###&#"'##''(('#&&   '(##'((!    %
Check your data and re-run preprocess with the correct quality scaling flag.
[a5] Error preprocessing reads with SGA

Original comment by piyuve...@gmail.com on 3 Sep 2013 at 9:48

[GoogleCodeExporter]

Reported by hiren.ghosh@gmail.com

I am also getting same error. I am using illumina pair end read: 
[a5] Begin: 8:51 on 10-1-2013
[a5] Found the following libraries:
     raw1:
      id=raw1
      p1=ResetH10_S1_L001_R1_001.fastq
      p2=ResetH10_S1_L001_R2_001.fastq
[a5] Found 1 libraries
[a5] Starting pipeline at step 1
[a5] Cleaning reads with SGA
[a5] Cleaning reads with SGA
preprocess: WARNING - it is suggested that the min read length is 40
preprocess: Using very short reads may considerably impact the performance
Parameters:
QualTrim: 10
QualFilter: at most 20 low quality bases
HardClip: 0
Min length: 29
Sample freq: 1
PE Mode: 0
Quality scaling: 3
MinGC: 0
MaxGC: 1
Outfile: stdout
Processing ResetH10_S1_L001_R1_001.fastq

Error: read M00815:32:000000000-A4TKR:1:1101:16739:1715 has out of range 
quality values.
Expected phred64.
Quality string: """"""'#''#(& &&&' ')$()''()%('#'"'"&$ 
&$()')#''#%%#'#(&'((((!'&''($& &)'$(#$&& &#!''#$ #( 
%''#'))$!('"$(((&'$$$&$#'''##"''"'##"#"&"
####' "## !!##
Check your data and re-run preprocess with the correct quality scaling flag.
[a5] Error preprocessing reads with SGA

Original comment by hiren.gh...@gmail.com on 1 Nov 2013 at 7:54