#340 runCa error

[lamiaa lahlou]

Hello
when i use this command line
runCA -p ypestis -d ypestis-raw useGrid=1 scriptOnGrid=1 doOBT=1 unitigger=bogart READS-sra/SRR133640.frg
runCA -p ypestis -d ypestis-corrected useGrid=1 scriptOnGrid=1 doOBT=0 unitigger=bogart READS-sra/SRR133640.corrected.frg
i have an error telling qsub not found?
Plz help me

[Brian Walenz]

Do you have SGE installed? If no, leave out "useGrid=1 scriptOnGrid=1". If yes, ask someone at your site for help setting it up.

[lamiaa lahlou]

thank you i trid it but i have another error .

GKP finished with 1828231 alerts or errors:
1828231 # ILL Error: seq longer than longer than gkpShortReadLength bases, truncating.

ERROR: library IID 1 'SRR133640' has 82.68% errors or warnings.

---

Failure message:

gatekeeper failed

Give me a sollution plz

[Sergey Koren]

It sounds like your frg is incorrect or your data is bad. The frg file specifies that the reads are <160bp. Looking at this SRA id, the reads are 100bp but your input file is >160bp which I think means you didn’t process the SRA file properly or have another fastq error. You can download the fastq directly from EBI:
http://www.ebi.ac.uk/ena/data/view/SRR133640&display=html

That said, CA is no longer supported so any bugs you find won’t get fixed and it was never recommended for Illumina-only assembly.

On May 6, 2016, at 6:49 AM, lamiaa lahlou lamiaa11@users.sf.net wrote:

thank you i trid it but i have another error .

GKP finished with 1828231 alerts or errors:
1828231 # ILL Error: seq longer than longer than gkpShortReadLength bases, truncating.

ERROR: library IID 1 'SRR133640' has 82.68% errors or warnings.

Failure message:

gatekeeper failed

Give me a sollution plz

[bugs:#340] https://sourceforge.net/p/wgs-assembler/bugs/340/ runCa error

Status: open
Group: consensus
Created: Fri May 06, 2016 09:23 AM UTC by lamiaa lahlou
Last Updated: Fri May 06, 2016 10:39 AM UTC
Owner: nobody

Hello
when i use this command line
runCA -p ypestis -d ypestis-raw useGrid=1 scriptOnGrid=1 doOBT=1 unitigger=bogart READS-sra/SRR133640.frg
runCA -p ypestis -d ypestis-corrected useGrid=1 scriptOnGrid=1 doOBT=0 unitigger=bogart READS-sra/SRR133640.corrected.frg
i have an error telling qsub not found?
Plz help me

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