Question: masurca error in close gaps
gravatar for Arthur Melo
5.4 years ago by
Arthur Melo0 wrote:

Hello people,
I have any problem with Masurca assembler. I think that problem is in Jellyfish step.
The error is related with close gaps: "Gap close failed, you can still use pre-gap close files under CA/9-terminator/. Check gepClose.err for problems"

Cheking gepClose.err ...

mkdir CA/10-gapclose
outputDirectory = CA/10-gapclose
/usr/local/MaSuRCA- /home/lays/jatoba/dados_norm/masurca/CA/9-terminator 51 200
/usr/local/MaSuRCA- /home/lays/jatoba/dados_norm/masurca/CA/9-terminator 51 > /home/lays/jatoba/dados_norm/masurca/CA/10-gapclose/contig_end_pairs.51.fa
/usr/local/MaSuRCA- /home/lays/jatoba/dados_norm/masurca/CA/9-terminator 200 > /home/lays/jatoba/dados_norm/masurca/CA/10-gapclose/contig_end_pairs.200.fa
/usr/local/MaSuRCA- /home/lays/jatoba/dados_norm/masurca/CA/9-terminator --contig-end-seq-file /home/lays/jatoba/dados_norm/masurca/CA/10-gapclose/contig_end_pairs.51.fa > gap.insertMeanAndStdev.txt
echo "cc 600 200" >
jellyfish count -s 7000000000 -C -t 12 -m 21 -L 100 -o restrictKmers /home/lays/jatoba/dados_norm/masurca/pA.renamed.fastq /home/lays/jatoba/dados_norm/masurca/pB.renamed.fastq /home/lays/jatoba/dados_norm/masurca/pC.renamed.fastq /home/lays/jatoba/dados_norm/masurca/pD.renamed.fastq
ln -sf restrictKmers_0 restrictKmers
jellyfish dump -L 1000 restrictKmers -c > highCountKmers.txt
jellyfish count -s 1 -C -t 12 -m 21 -o fishingAll /home/lays/jatoba/dados_norm/masurca/CA/10-gapclose/contig_end_pairs.200.fa
terminate called after throwing an instance of 'jellyfish::file_parser::FileParserError'
what(): Empty input file '/home/lays/jatoba/dados_norm/masurca/CA/10-gapclose/contig_end_pairs.200.fa'
child died with signal 6, with coredump

The algorithm doesn't create the file "contig_end_paird.200.fa". What it means? 
Someone can help me?

Thanks a lot ...

assembly • 1.6k views
ADD COMMENTlink modified 5.2 years ago by Biostar ♦♦ 20 • written 5.4 years ago by Arthur Melo0
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