#270 Gatekeepe error with 181bp illu reads

[Won Cheol Yim]

Dear All,
I try to run CA8.1 for my illumina reads. (PE x 181bp)
But I got this error message.
Can you help me to ran CA?
Thank you.
Won
===========
Starting file '/scratch/wyim/iceplant/wgs/ca/pe.frg'.
Processing INNIE ILLUMINA 1.3+ QV encoding reads from:
'/home/wyim/scratch/iceplant/wgs/source/ec_fastq/ec.paired.A.fastq'
and '/home/wyim/scratch/iceplant/wgs/source/ec_fastq/ec.paired.B.fastq'
GKP finished with 768389442 alerts or errors:
441945432 # ILL Error: seq longer than longer than gkpShortReadLength bases, truncating.
326444009 # ILL Alert: invalid QV in read.
1 # LIB Alert: suspicious mean and standard deviation; reset stddev to 0.10 * mean.
ERROR: library IID 1 'pe_long' has 154.07% errors or warnings.

[Brian Walenz]

Use -technology illumina-long for reads longer than 160bp.

The 'invalid QV' is caused by an incorrect -type setting. 'fastqAnalyze ec.paired.A.fastq' should give a guess as to what the correct setting is. I will guess you want 'sanger' here.

For reference on the QV's, see http://en.wikipedia.org/wiki/FASTQ_format

[Brian Walenz]

Closing case.