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  • xiaenhua
    started a topic Trouble with NovelSeq!

    Trouble with NovelSeq!

    Hi,everyone
    i had some trouble when running NovelSeq(http://compbio.cs.sfu.ca/novelseq/manual.html). As we know, NovelSeq is a pepiline that was designed to detect novel sequence insertions using paired-end next-generation sequencing. In my project, i am in trouble when running novel_cluster. Before running the novel_cluster program, i had mapped the illumina pair-end reads (42X72bp) to the O.sativa_japonica genome using mrfast, and got the output files including: OEA alignment file (SAM), unmapped reads(Orphan) (fastq) and the OEA sequences fasta file. Then i assemblied the Orphan reads into contigs by using the ABySS package. Following the manual of NovelSeq, now i must cluster the OEA reads and localy assembly the OEA clusters using novelseq_cluster program, i prepared all the input files needed for novelseq_cluster, then running..., unluckly, it shows some errors, i also checked the input files again, and didn't find any error. Un..
    who can give me some advices? Great appreciate for your any kind help!
    the error info is as below:
    ------------------------
    xiaenhua@node69: ~/Alignment_Tools/novelseq-upload/novel_cluster /home/xiaenhua/Novel_Seq/gla/3_OEACluster/novelseq-upload/ ../gla_OEA.sam ../satRemChrs.txt ../Chr_length/ ../gla_OEA.fa ../histogram.txt 100
    ./parserQualWReadPrunWSatellite /home/xiaenhua/Novel_Seq/gla/3_OEACluster/novelseq-upload//../gla_OEA.sam /home/xiaenhua/Novel_Seq/gla/3_OEACluster/novelseq-upload//../satRemChrs.txt > ../gla_OEA.sam.parsed
    cut -f1 ../gla_OEA.sam.parsed > ../gla_OEA.sam.Name
    ./unique ../gla_OEA.sam.Name > ../gla_OEA.sam.Name.Unique
    ./sortString ../gla_OEA.sam.Name.Unique > ../gla_OEA.sam.Name.Unique.sort
    cut -f1,6,8 ../gla_OEA.sam.parsed > ../gla_OEA.sam.Name.Edit.Prob
    ./calProbMinEditRead ../gla_OEA.sam.Name.Unique.sort ../gla_OEA.sam.Name.Edit.Prob > ../gla_OEA.sam.Name.MinEdit.TotalProb
    sh: line 1: 20325 Segmentation fault ./calProbMinEditRead ../gla_OEA.sam.Name.Unique.sort ../gla_OEA.sam.Name.Edit.Prob >../gla_OEA.sam.Name.MinEdit.TotalProb
    ./convertToInvLRProbMinEditDist ../gla_OEA.sam.parsed $dataset.Name.MinEdit.TotalProb > ../gla_OEA.sam.parsed.LR
    sh: line 1: 20327 Segmentation fault ./convertToInvLRProbMinEditDist ../gla_OEA.sam.parsed $dataset.Name.MinEdit.TotalProb >../gla_OEA.sam.parsed.LR
    ./OEASetsProb ../Chr_length//chroName1 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr1
    ./OEASetsProb ../Chr_length//chroName2 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr2
    ./OEASetsProb ../Chr_length//chroName3 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr3
    ./OEASetsProb ../Chr_length//chroName4 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr4
    ./OEASetsProb ../Chr_length//chroName5 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr5
    ./OEASetsProb ../Chr_length//chroName6 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr6
    ./OEASetsProb ../Chr_length//chroName7 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr7
    ./OEASetsProb ../Chr_length//chroName8 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr8
    ./OEASetsProb ../Chr_length//chroName9 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr9
    ./OEASetsProb ../Chr_length//chroName10 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr10
    ./OEASetsProb ../Chr_length//chroName11 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr11
    ./OEASetsProb ../Chr_length//chroName12 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr12
    ./OEASetsProb ../Chr_length//chroName13 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr13
    ./OEASetsProb ../Chr_length//chroName14 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr14
    ./OEASetsProb ../Chr_length//chroName15 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr15
    ./OEASetsProb ../Chr_length//chroName16 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr16
    ./OEASetsProb ../Chr_length//chroName17 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr17
    ./OEASetsProb ../Chr_length//chroName18 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr18
    ./OEASetsProb ../Chr_length//chroName19 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr19
    ./OEASetsProb ../Chr_length//chroName20 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr20
    ./OEASetsProb ../Chr_length//chroName21 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr21
    ./OEASetsProb ../Chr_length//chroName22 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr22
    ./OEASetsProb ../Chr_length//chroName23 ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chr23
    ./OEASetsProb ../Chr_length//chroNameX ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chrX
    ./OEASetsProb ../Chr_length//chroNameY ../gla_OEA.sam.parsed.LR ../gla_OEA.sam.parsed.chrY
    cat ../gla_OEA.sam.parsed.chr? >> ../gla_OEA.sam.parsed.AllChr
    cat ../gla_OEA.sam.parsed.chr?? >> ../gla_OEA.sam.parsed.AllChr
    ./setCoverProbWeighted ../gla_OEA.sam.Name.Unique.sort ../gla_OEA.sam.parsed.AllChr
    ./type1to2convertor ../gla_OEA.sam.parsed.AllChr ../gla_OEA.fa
    sh: ./fs-fa.out: No such file or directory
    ./oea.LocalAssembly ../histogram.txt ../gla_OEA.sam.parsed.AllChr.type2 100
    sh: ./oea.LocalAssembly: No such file or directory
    --------------------
    Note:my working dir is :
    /home/xiaenhua/Novel_Seq/gla/3_OEACluster/novelseq-upload/
    (the same as NovelSeq Install dir)

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