Question: deconseq syntax error
0
gravatar for sara.zahran
9 months ago by
sara.zahran0 wrote:

Hello, I am trying to removal human sequences from metagenome sequences using deconseq-standalone-0.4.3, first I downloaded hs_ref_GRCh37 conseq databases s1, s2 and s3 then I modified the deconseqconfig.pm as follows:

 use constant DBS => {hsref => {name => 'hs_ref_GRCh37_s1','hs_ref_GRCh37_s2','hs_ref_GRCh37_s3',
                       db => 'hs_ref_GRCh37_s1,hs_ref_GRCh37_s2,hs_ref_GRCh37_s3'},
                        bact => {name => 'Viral genomes',
                                db => 'bactDB'}};

but I got an error as follows:

syntax error at /home/deconseq-standalone-0.4.3/DeconSeqConfig.pm line 20 near "db"
BEGIN not safe after errors--compilation aborted at /home/deconseq-standalone-0.4.3/DeconSeqConfig.pm line 25
compilation failed in require at /home/deconseq-standalone-0.4.3/deconseq.pl line 26
BEGIN failed--compilation aborted at /home/deconseq-standalone-0.4.3/deconseq.pl line 26

I am not an expert in perl language and i am using virtualbox

how can i deal with these errors

thanks in advance

software error • 311 views
ADD COMMENTlink modified 9 months ago by WouterDeCoster40k • written 9 months ago by sara.zahran0
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ADD REPLYlink written 9 months ago by WouterDeCoster40k
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