Closed rene-rex closed 10 years ago
I'm travelling at the moment - will look at fixing num_reads > 0
issue on Monday. Sorry about that.
For the second issue, the contig
command only pulls out contigs for a single sample at a time. So you probably want to do:
ctx63 contigs -m 150G -t 10 -c 1 -p 1:genotype1.ctp.gz --out contigs1.fa refAndSamples.clean.ctx
ctx63 contigs -m 150G -t 10 -c 2 -p 2:genotype1.ctp.gz --out contigs2.fa refAndSamples.clean.ctx
Hope that helps. Thank you for trying cortex.
Isaac
Hi
Thanks for the answer. I tried the first command
ctx63 contigs -m 150G -t 10 -c 1 -p 1:genotype1.ctp.gz --out contigs1.fa refAndSamples.clean.ctx
but it produced another error:
[src/graph_paths/gpath_checks.c:107] Error graphs_gpaths_compatible(): Sample names don't match
refAndSamples.clean.ctx:0reference
refAndSamples.clean.ctx:2genotype2.tipclean.supclean7
[22 Aug 2014 08:19:32-JOC] Fatal Error
Is it comparing the names of different samples in the same file?
I'm trying to resolve this issue at the moment. For now you should be able to work around it by only loading one sample at a time. This is not ideal, but I'll put up a fix shortly.
ctx63 contigs -m 150G -t 10 -c 0 -p genotype1.ctp.gz --out contigs1.fa refAndSamples.clean.ctx:1
Hello
I tried to follow the "Workflow Examples" in the wiki to do variant calling with two plant genotypes based on paired end reads. Here is the sequence of commands I used:
Unfortunately, both read threading steps failed with this error:
I tried to "fix" this by adding this code above line 135 in alignment/correct_aln_stats.c:
After recompiling the threading runs smooth. However, now I am stuck at the contigs command
which yields:
Any clues what went wrong?