Question: defuse running error message
0
gravatar for esraesmeray1990
11 months ago by
Izmir Biomedicine and Genome Center
esraesmeray199010 wrote:

I am trying to run defuse tool but ı am taking following error message i am kind of new so i really dont understand what is the probem. If anyone help me i will be appreciate .

esra@asus:/media/esra/Data$ defuse_run.pl -d dataset_directory -1 read1.fq.gz -2 read2.fq.gz -o output_dir
    [2019-01-30 13:39:52]  Starting deFuse v0.7.0 for files read1.fq.gz and read2.fq.gz
    [2019-01-30 13:39:52]  Importing fastq files [1078 sec]
    [2019-01-30 13:57:50]  Splitting fastq files [911 sec]
    [2019-01-30 14:13:01]  Discordant alignmentsFailure for defuse command:
        /home/esra/anaconda3/opt/defuse/scripts/alignjob.pl -c /home/esra/anaconda3/opt/defuse/scripts/config.txt -d dataset_directory -j reads.split.010 -l /media/esra/Data/output_dir/tmp -o /media/esra/Data/output_dir -n output_dir -p /media/esra/Data/output_dir/jobs/reads.split.010 
    Reason:
        Job command with nonzero return code
    Job output:
        Running on asus
        Error: Required file dataset_directory/defuse.cdna.fa does not exist
        Starting alignjob reads.split.010

        real    0m0,054s
        user    0m0,039s
        sys 0m0,008s
    Return codes: 2
    Failure for defuse command:
        /home/esra/anaconda3/opt/defuse/scripts/alignjob.pl -c /home/esra/anaconda3/opt/defuse/scripts/config.txt -d dataset_directory -j reads.split.009 -l /media/esra/Data/output_dir/tmp -o /media/esra/Data/output_dir -n output_dir -p /media/esra/Data/output_dir/jobs/reads.split.009 
    Reason:
        Job command with nonzero return code
    Job output:
        Running on asus
        Error: Required file dataset_directory/defuse.cdna.fa does not exist
        Starting alignjob reads.split.009

        real    0m0,046s
        user    0m0,041s
        sys 0m0,004s
    Return codes: 2
    Failure for defuse command:
        /home/esra/anaconda3/opt/defuse/scripts/alignjob.pl -c /home/esra/anaconda3/opt/defuse/scripts/config.txt -d dataset_directory -j reads.split.008 -l /media/esra/Data/output_dir/tmp -o /media/esra/Data/output_dir -n output_dir -p /media/esra/Data/output_dir/jobs/reads.split.008 
    Reason:
        Job command with nonzero return code
    Job output:
        Running on asus
        Error: Required file dataset_directory/defuse.cdna.fa does not exist
        Starting alignjob reads.split.008

        real    0m0,043s
        user    0m0,039s
        sys 0m0,004s
    Return codes: 2
    Failure for defuse command:
        /home/esra/anaconda3/opt/defuse/scripts/alignjob.pl -c /home/esra/anaconda3/opt/defuse/scripts/config.txt -d dataset_directory -j reads.split.007 -l /media/esra/Data/output_dir/tmp -o /media/esra/Data/output_dir -n output_dir -p /media/esra/Data/output_dir/jobs/reads.split.007 
    Reason:
        Job command with nonzero return code
    Job output:
        Running on asus
        Error: Required file dataset_directory/defuse.cdna.fa does not exist
        Starting alignjob reads.split.007

        real    0m0,045s
        user    0m0,044s
        sys 0m0,000s
    Return codes: 2
    Failure for defuse command:
        /home/esra/anaconda3/opt/defuse/scripts/alignjob.pl -c /home/esra/anaconda3/opt/defuse/scripts/config.txt -d dataset_directory -j reads.split.006 -l /media/esra/Data/output_dir/tmp -o /media/esra/Data/output_dir -n output_dir -p /media/esra/Data/output_dir/jobs/reads.split.006 
    Reason:
        Job command with nonzero return code
    Job output:
        Running on asus
        Error: Required file dataset_directory/defuse.cdna.fa does not exist
        Starting alignjob reads.split.006

        real    0m0,047s
        user    0m0,046s
        sys 0m0,000s
    Return codes: 2
    Failure for defuse command:
        /home/esra/anaconda3/opt/defuse/scripts/alignjob.pl -c /home/esra/anaconda3/opt/defuse/scripts/config.txt -d dataset_directory -j reads.split.005 -l /media/esra/Data/output_dir/tmp -o /media/esra/Data/output_dir -n output_dir -p /media/esra/Data/output_dir/jobs/reads.split.005 
    Reason:
        Job command with nonzero return code
    Job output:
        Running on asus
        Error: Required file dataset_directory/defuse.cdna.fa does not exist
        Starting alignjob reads.split.005

        real    0m0,046s
        user    0m0,037s
        sys 0m0,008s
    Return codes: 2
    Failure for defuse command:
        /home/esra/anaconda3/opt/defuse/scripts/alignjob.pl -c /home/esra/anaconda3/opt/defuse/scripts/config.txt -d dataset_directory -j reads.split.004 -l /media/esra/Data/output_dir/tmp -o /media/esra/Data/output_dir -n output_dir -p /media/esra/Data/output_dir/jobs/reads.split.004 
    Reason:
        Job command with nonzero return code
    Job output:
        Running on asus
        Error: Required file dataset_directory/defuse.cdna.fa does not exist
        Starting alignjob reads.split.004

        real    0m0,046s
        user    0m0,045s
        sys 0m0,000s
    Return codes: 2
    Failure for defuse command:
        /home/esra/anaconda3/opt/defuse/scripts/alignjob.pl -c /home/esra/anaconda3/opt/defuse/scripts/config.txt -d dataset_directory -j reads.split.003 -l /media/esra/Data/output_dir/tmp -o /media/esra/Data/output_dir -n output_dir -p /media/esra/Data/output_dir/jobs/reads.split.003 
    Reason:
        Job command with nonzero return code
    Job output:
        Running on asus
        Error: Required file dataset_directory/defuse.cdna.fa does not exist
        Starting alignjob reads.split.003

        real    0m0,048s
        user    0m0,048s
        sys 0m0,000s
    Return codes: 2
    Failure for defuse command:
        /home/esra/anaconda3/opt/defuse/scripts/alignjob.pl -c /home/esra/anaconda3/opt/defuse/scripts/config.txt -d dataset_directory -j reads.split.002 -l /media/esra/Data/output_dir/tmp -o /media/esra/Data/output_dir -n output_dir -p /media/esra/Data/output_dir/jobs/reads.split.002 
    Reason:
        Job command with nonzero return code
    Job output:
        Running on asus
        Error: Required file dataset_directory/defuse.cdna.fa does not exist
        Starting alignjob reads.split.002

        real    0m0,046s
        user    0m0,042s
        sys 0m0,004s
    Return codes: 2
    Failure for defuse command:
        /home/esra/anaconda3/opt/defuse/scripts/alignjob.pl -c /home/esra/anaconda3/opt/defuse/scripts/config.txt -d dataset_directory -j reads.split.001 -l /media/esra/Data/output_dir/tmp -o /media/esra/Data/output_dir -n output_dir -p /media/esra/Data/output_dir/jobs/reads.split.001 
    Reason:
        Job command with nonzero return code
    Job output:
        Running on asus
        Error: Required file dataset_directory/defuse.cdna.fa does not exist
        Starting alignjob reads.split.001

        real    0m0,048s
        user    0m0,043s
        sys 0m0,004s
    Return codes: 2
    Failure for defuse command:
        /home/esra/anaconda3/opt/defuse/scripts/alignjob.pl -c /home/esra/anaconda3/opt/defuse/scripts/config.txt -d dataset_directory -j reads.split.000 -l /media/esra/Data/output_dir/tmp -o /media/esra/Data/output_dir -n output_dir -p /media/esra/Data/output_dir/jobs/reads.split.000 
    Reason:
        Job command with nonzero return code
    Job output:
        Running on asus
        Error: Required file dataset_directory/defuse.cdna.fa does not exist
        Starting alignjob reads.split.000

        real    0m0,045s
        user    0m0,044s
        sys 0m0,000s
    Return codes: 2
    11 commands failed after 12 seconds
defuse software error • 386 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by esraesmeray199010
1

How did you install defuse ?

The error is Error: Required file dataset_directory/defuse.cdna.fa does not exist

Did you check that directory ? Is defuse.cdna.fa in there ?

More here : A problem about the download of the human genome in defuse

ADD REPLYlink modified 11 months ago • written 11 months ago by Bastien Hervé4.5k

I used anaconda to install defuse:

  esra@asus:~$ conda install -c dranew defuse

Yes defuse.cdna.fa is in dataset_directory and files are not empty. Download the Reference Dataset:

esra@asus:~$ defuse_create_ref.pl -d dataset_directory 
esra@asus:~/dataset_directory$ ls
defuse.cdna.fa                defuse.dna.chromosomes.3.fa   est.5.fa
defuse.cdna.fa.1.ebwt         defuse.dna.chromosomes.4.fa   est.6.fa
defuse.cdna.fa.2.ebwt         defuse.dna.chromosomes.5.fa   est.7.fa
defuse.cdna.fa.3.ebwt         defuse.dna.chromosomes.6.fa   est.8.fa
defuse.cdna.fa.4.ebwt         defuse.dna.chromosomes.7.fa   est.9.fa
defuse.cdna.fa.fai            defuse.dna.chromosomes.8.fa   est.fa
defuse.cdna.fa.rev.1.ebwt     defuse.dna.chromosomes.9.fa   gmap
defuse.cdna.fa.rev.2.ebwt     defuse.dna.chromosomes.MT.fa  Homo_sapiens.GRCh37.69.dna.chromosomes.fa
defuse.cdna.regions           defuse.dna.chromosomes.X.fa   Homo_sapiens.GRCh37.69.dna.chromosomes.fa.1.ebwt
defuse.cds.fa                 defuse.dna.chromosomes.Y.fa   Homo_sapiens.GRCh37.69.dna.chromosomes.fa.2.ebwt
defuse.cds.fa.2bit            defuse.exons.fa               Homo_sapiens.GRCh37.69.dna.chromosomes.fa.3.ebwt
defuse.dna.chromosomes.10.fa  defuse.exons.fa.2bit          Homo_sapiens.GRCh37.69.dna.chromosomes.fa.4.ebwt
defuse.dna.chromosomes.11.fa  defuse.ig.gene.list           Homo_sapiens.GRCh37.69.dna.chromosomes.fa.index
defuse.dna.chromosomes.12.fa  defuse.reference.fa           Homo_sapiens.GRCh37.69.dna.chromosomes.fa.rev.1.ebwt
defuse.dna.chromosomes.13.fa  defuse.reference.fa.fai       Homo_sapiens.GRCh37.69.dna.chromosomes.fa.rev.2.ebwt
defuse.dna.chromosomes.14.fa  defuse.rrna.fa                Homo_sapiens.GRCh37.69.gtf
defuse.dna.chromosomes.15.fa  defuse.rrna.fa.1.ebwt         Hs.seq.uniq
defuse.dna.chromosomes.16.fa  defuse.rrna.fa.2.ebwt         Hs.seq.uniq.1.ebwt
defuse.dna.chromosomes.17.fa  defuse.rrna.fa.3.ebwt         Hs.seq.uniq.2.ebwt
defuse.dna.chromosomes.18.fa  defuse.rrna.fa.4.ebwt         Hs.seq.uniq.3.ebwt
defuse.dna.chromosomes.19.fa  defuse.rrna.fa.rev.1.ebwt     Hs.seq.uniq.4.ebwt
defuse.dna.chromosomes.1.fa   defuse.rrna.fa.rev.2.ebwt     Hs.seq.uniq.rev.1.ebwt
defuse.dna.chromosomes.20.fa  est.1.fa                      Hs.seq.uniq.rev.2.ebwt
defuse.dna.chromosomes.21.fa  est.2.fa                      intronEst.txt
defuse.dna.chromosomes.22.fa  est.3.fa                      repeats.regions
defuse.dna.chromosomes.2.fa   est.4.fa                      repeats.txt

Then i just run the following command:

 defuse_run.pl -d dataset_directory -1 read1.fq.gz -2 read2.fq.gz -o output_dir
ADD REPLYlink modified 11 months ago • written 11 months ago by esraesmeray199010

Is this command line working better ?

defuse_run.pl -d ~/dataset_directory -1 read1.fq.gz -2 read2.fq.gz -o output_dir

From esra@asus:/media/esra/Data$

Because I suspect you don't have the dataset_directory under esra@asus:/media/esra/Data$

ADD REPLYlink modified 11 months ago • written 11 months ago by Bastien Hervé4.5k

Hi,

I tried but it gives the same error :(

   defuse_run.pl -d ~/dataset_directory -1 read1.fq.gz -2 read2.fq.gz -o output_dir
ADD REPLYlink written 11 months ago by esraesmeray199010

Could you please try to ls where you run defuse_run.pl

ADD REPLYlink written 11 months ago by Bastien Hervé4.5k
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