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bioinfologics / w2rap-contigger

An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes.
http://bioinfologics.github.io/the-w2rap-contigger/
MIT License
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Some trouble with CP_MAX_QDIFF value ! #5

Closed Arno75 closed 8 years ago

Arno75 commented 8 years ago

Hello, i've try to run w2rap-contigger on my illumina data set. The first steps (01_unipaths, 02_qgraph and 03_clean) are ok. But in the patching process , i've got some trouble with CP_MAX_QDIFF value, and this message in the output "Illegal value for CP_MAX_QDIFF". This variable is define in the patching script , and can't be modified. Thanks in advance for your help.

Arnaud

gonzalogacc commented 8 years ago

Hi Arnaud. Can you describe your data a bit? Insert size distribution, kmer spectra, quality profile, duplication rate, etc. Did you try to modify the variable value? Best. Gonza.-

Arno75 commented 8 years ago

It's a Paired End (2X300pb - Insert Size ~ 600pb) library, for an eukaryotic genome (heterozygous) of 1,5Gb Size. The duplication rate is less than 1% and the average quality score is near 31. Yes i've tryed to modify it , but it has no effect. I do not understand exactly what it does. The maximum accepted quality difference between two reads of a pair??? ... i suppose.

bjclavijo commented 8 years ago

What is your rationale to modify this? this is the maximum discrepancy between a pair and the rest of the cluster for read correction.

Arno75 commented 8 years ago

I have no real reason to modife this variable , it's already define in the script. But the error message said that it's an illegal value.

bjclavijo commented 8 years ago

Ok, so you are not modifying the code at all and when running you're getting that error? As far as I know we haven't changed anything on that part of the code for a while. Can you tell us which compiler, os, etc you're using? If you made any modifications at all to the code, that would be needed too, as a full transcript of the output error.

Arno75 commented 8 years ago

GCC: (GNU) 4.4.7

and this is the entire error message ...

Set computational resources SYSTEM INFO

mar. mai 24 17:45:51 2016: finding unsatisfieds mar. mai 24 17:46:22 2016: creating multiplicity std::map mar. mai 24 17:46:24 2016: economizing links mar. mai 24 17:46:25 2016: forming neighborhoods mar. mai 24 17:47:34 2016: forming initial clusters mar. mai 24 17:47:52 2016: start sort 1.86 seconds used sorting mar. mai 24 17:47:54 2016: merging clusters xs.size( ) = 3519942 6.96 minutes used merging xs.size( ) = 1553913 mar. mai 24 17:55:03 2016: start overlap-based merging mar. mai 24 18:00:41 2016: start overlap-based merging LR.size( ) = 1500659 LR.size( ) = 750897 mar. mai 24 18:08:35 2016: now processing 750897 blobs mar. mai 24 18:08:35 2016: memory in use = 21.25 GB, peak = 20.76 GB

Fatal error (pid=119313) at mar. mai 24 18:08:35 2016: Illegal value for CP_MAX_QDIFF.

gonzalogacc commented 8 years ago

Have you modified the CP_MAX_QDIFF variable at any point?

Arno75 commented 8 years ago

No, at the beginning i do not ! But after reading this error message , i tried to change it whithout succes.

gonzalogacc commented 8 years ago

Try using Gcc 5.2+ and let me know how it goes.

bjclavijo commented 8 years ago

Hi Arnaud, any news on this?

bjclavijo commented 8 years ago

Hi Arnaud, as I have not heard back I'll close this one, If there are still any problems you can comment here and we'll re-open this if needed.