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ploteig calls /home/np29/bin/fixgreen #13

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ddrichel opened this issue Oct 5, 2016 · 7 comments
Open

ploteig calls /home/np29/bin/fixgreen #13

ddrichel opened this issue Oct 5, 2016 · 7 comments

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@ddrichel
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ddrichel commented Oct 5, 2016

No description provided.

@muhammadsohailraza
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muhammadsohailraza commented Nov 16, 2016

Hi,
I use ploteig.pl to draw the plots from EIGENSOFT's example data, but i got following error, can anyone please help me to fix this issue: Thanks!
command-line:
./ploteig.pl -i example.eval -c 1:2 -p Case:Control -x -y -o sohail.plot

##Error:
number of fields: 1
Case:Control
line 0: warning: Skipping data file with no valid points
line 0: warning: Skipping data file with no valid points

gnuplot> plot "/leofs/zengchq_group/sohail/softwares/Eigensoft/EIG-6.1.4/TEST/example.eval.1:2:Case" using ($2)_1:($3)_1 title "Case" , "/leofs/zengchq_group/sohail/softwares/Eigensoft/EIG-6.1.4/TEST/example.eval.1:2:Control" using ($2)_1:($3)_1 title "Control"
^
line 0: x range is invalid

Can't exec "/home/np29/bin/fixgreen": No such file or directory at ./ploteig.pl line 138, line 5.

@bumblenick
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  1. Please comment out or remove the call to fixgreen
    (My bad)
  2. Please check very carefully that the last column of the evec file has
    entries Case or Control
  3. If 2) is OK make a file casecontrol with 2 lines Case aand Control and
    change the Case:Control to caseconttrol

Sorry to put you through this.

Nick

On Wed, Nov 16, 2016 at 3:53 AM, SOHAIL [email protected] wrote:

Hi,
I use ploteig.pl to draw the plots from EIGENSOFT's example data, but i
got following error, can anyone please help me to fix this issue: Thanks!
command-line:
./ploteig2.pl -i example.eval -c 1:2 -p Case:Control -x -y -o sohail.plot

##Error:
number of fields: 1
Case:Control
line 0: warning: Skipping data file with no valid points
line 0: warning: Skipping data file with no valid points

gnuplot> plot "/leofs/zengchq_group/sohail/softwares/Eigensoft/EIG-6.1.4/TEST/example.eval.1:2:Case"
using ($2)_1:($3)_1 title "Case" , "/leofs/zengchq_group/sohail/
softwares/Eigensoft/EIG-6.1.4/TEST/example.eval.1:2:Control" using ($2)
_1:($3)_1 title "Control"
^
line 0: x range is invalid

Can't exec "/home/np29/bin/fixgreen": No such file or directory at ./
ploteig1.pl line 138, line 5.


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@muhammadsohailraza
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Thank you @nick!

@farnushfarhadi
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Hi,

I am running in to the same problem :

The command is

smartpca.perl -i tmp/GenomTranscriptomTwinsMD_c1_QC_pruned_IBD.ped -a tmp/GenomTranscriptomTwinsMD_c1_QC_pruned_IBD.map -b tmp/GenomTranscriptomTwinsMD_c1_QC_pruned_IBD.fam -s 6 -e out/eval -l out/elog -o out/pca -p out/plot

The error is

ploteig -i out/pca.evec -c 1:2 -p Control -x -y -o out/plot.xtxt

number of fields: 12

Control
Can't exec "/home/np29/bin/fixgreen": No such file or directory at /usr/local/bin/ploteig line 138, line 1984.
evec2pca-ped.perl 10 out/pca.evec tmp/GenomTranscriptomTwinsMD_c1_QC_pruned_IBD.fam out/pca

Shall I do the same thing you suggested above? I.e., commenting "system "/home/np29/bin/fixgreen $psfile" ;" in ploteig file?

@bumblenick
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bumblenick commented Jun 8, 2017 via email

@farnushfarhadi
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Thank you.
I have commented the corresponding line but still I get the error. Am I missing anything?

@bumblenick
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bumblenick commented Jun 9, 2017 via email

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