parallel STRUCTURE

[Júnior Nadaline]

Hello structure users

 I'm attempting to use the CIPRES Gateway to run STRUCTURE on UCEs  markers. When I go to run the analysis, I obtain this error message:

Loading required package: parallel
Error in file(file, "rt") : cannot open the connection
Calls: parallel_structure -> plot_str -> as.matrix -> read.table -> file
In addition: Warning messages:
1: strings not representable in native encoding will be translated to UTF-8 
2: In file(file, "rt") :
  cannot open file './results_job_T1_q': No such file or directory
Execution halted
srun: error: comet-10-50: task 0: Exited with exit code 1

My data is 27548 filtered SNPs (GATK pipelines), here is the partial summary of my input data:

pop4_48mc	4	0	0	... continue
pop4_48mc	4	1	1	... continue
pop4_49mc	4	0	0	... continue
pop3_49ga	3	1	1	... continue
pop3_50ga	3	0	0	... continue
... continue

And the jobfile:

T1 1,2,3,4,5,6 4 1000 10000
T2 1,2,3,4,5,6 4 1000 10000
T3 1,2,3,4,5,6 4 1000 10000
T4 1,2,3,4,5,6 4 1000 10000
T5 1,2,3,4,5,6 4 1000 10000
T6 1,2,3,4,5,6 4 1000 10000
T7 1,2,3,4,5,6 4 1000 10000
T8 1,2,3,4,5,6 4 1000 10000
T9 1,2,3,4,5,6 4 1000 10000
T10 1,2,3,4,5,6 4 1000 10000
T11 1,2,3,4,5,6 3 1000 10000
T12 1,2,3,4,5,6 3 1000 10000
T13 1,2,3,4,5,6 3 1000 10000
T14 1,2,3,4,5,6 3 1000 10000
T15 1,2,3,4,5,6 3 1000 10000
T16 1,2,3,4,5,6 3 1000 10000
T17 1,2,3,4,5,6 3 1000 10000
T18 1,2,3,4,5,6 3 1000 10000
T19 1,2,3,4,5,6 3 1000 10000

Can anyone help me to solve this issue?

 

Ps: Sorry about my english, if you don't understand something i can rewrite it.

Best Regards

--

Júnior Nadaline, Bsc

Currículum Lattes: http://lattes.cnpq.br/1358335903318855

MSc Student in Ecology and Conservation (UFPR)

Laboratory of Evolutionary Dynamics and Complex Systems  (pie-lab.org)

Curitiba, Paraná |Brazil

[Vikram Chhatre]

Hi Junior,

The error message is telling you where the problem could be:

cannot open file './results_job_T1_q': No such file or directory

It is probably something trivial such as lack of permissions to write this file in the current directory. You will need to speak with your system administrators to resolve issues with the local filesystem.  

V

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[Alice Mouton]

Hi Junior,

Did you resolve the situation with Cipres? I am getting the exact same error as well. It was running fine when I was saying that they all came from one population but I received errors when I add the sampling location and modify my joblist accordingly!

Many thanks for your help if you did manage to resolve it!

Alice