Issue with ParallelStructure

[Natalie Finnegan]

Hello! I have tried to troubleshoot this on my own but am having some difficulty. For reference, my most recent job handle is JobHandle=NGBW-JOB-PARALLELSTRUCTURE_XSEDE-C0C081CFEED94966AD96D4187F42B715

I am getting the error:

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: In read.table(data_name, colClasses = "character") : incomplete final line found by readTableHeader on 'data.txt' 2: In file(file, "rt") : cannot open file './results_job_T1_q': No such file or directory Execution halted srun: error: exp-4-35: task 0: Exited with exit code 1 srun: Terminating StepId=35616880.0

I am seeing that others in the google group had gotten this error and that it is a standard error that could be related to many formatting problems, but I am so stuck in trying to see what could be wrong with either my job file or data file.

I saw that another user had an issue with loci numbers, so I tried in this most recent iteration to remove the label column to ensure I was listing the right number of loci.

My job list is as follows:

T1 1,2,3,4 1 100000 500000 

T2 1,2,3,4 2 100000 500000 

T3 1,2,3,4 3 100000 500000 

T4 1,2,3,4 4 100000 500000 

T5 1,2,3,4 5 100000 500000 

T6 1,2,3,4 6 100000 500000

and my data list is pretty simple, large, but simple with only four taxa. I also have no population information, which I see can be an issue at times(?).

Any help anyone can offer would be great!

Natalie Finnegan

UCLA

[Pfeiffer, Wayne]

Hi Natalie,

I am concerned that you do not have a label at the beginning of each line in data.txt. All of the data.txt files that I have seen from other users have labels.

* What error did you get when you had labels?

Wayne

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[Natalie Finnegan]

That is a fair question!! I felt quite odd about it, but was trying to get something to work (and trying to see if I was somehow inputting the wrong number of loci). I was also concerned that when loading the same data into structure, there is a checkbox to hit that indicates there is a label column. Since I did not see anything explicitly like that in CIPRES, I figured I would try again without. When I did have labels, the error was:

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 message:
In file(file, "rt") :
  cannot open file './results_job_T1_q': No such file or directory
Execution halted
srun: error: exp-2-35: task 0: Exited with exit code 1
srun: Terminating StepId=35596789.0

[Pfeiffer, Wayne]

Hi Natalie,

Something to try would be to scale down the size of your data set to something really small to see if you could get the code to run. If that worked, then you could gradually add back some more data.

Incidentally, all of the command lines that I have seen from CIPRES users have popdata=1.

Wayne

[Miller, Mark]

Unfortunately, parallelstructure failures produce only one error message, the one you received.

The code just did not develop correct error messaging.

Wayne suggestion is a good one. It’s a place to start.

Let us know how that oges.

Mark

To view this discussion visit https://groups.google.com/d/msgid/cipres-science-gateway-users/49327AFC-3633-4929-80CE-845650F7C221%40sdsc.edu.

[Natalie Finnegan]

Hi all!

I got it working with popdata=1. I added a pop column and everything ran as expected (also, I added the labels back in). Just in case anyone has this issue in the future!

Thank you for the help!

Natalie

[Pfeiffer, Wayne]

Hi Natalie,

That’s great! Thanks for letting us know that the code is working for you now :)

Happy Holidays!

Wayne