Question: masurca error in close gaps
0
gravatar for Arthur Melo
5.4 years ago by
Brazil
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-2.0.3.1/bin/getEndSequencesOfContigs.perl /home/lays/jatoba/dados_norm/masurca/CA/9-terminator 51 200
/usr/local/MaSuRCA-2.0.3.1/bin/create_end_pairs.perl /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-2.0.3.1/bin/create_end_pairs.perl /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-2.0.3.1/bin/getMeanAndStdevForGapsByGapNumUsingCeleraAsmFile.perl /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" > meanAndStdevByPrefix.cc.txt
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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1636 users visited in the last hour