fastStructure: tuple index out of range

[Vikram Chhatre]

fastStructure experts:

I have hit the 'tuple out of range'  problem again with one of my data sets.  The set runs properly with original Structure program, but I am getting following error with fastStructure:

-------------------------------------------------------------------------------------------

$> python structure.py -K 2 --input=data1 --output=data1out --prior=simple

Traceback (most recent call last):

  File "~/fastSTRUCTURE/structure.py", line 165, in <module>

    G = parse_str.load(params['inputfile'])

  File "parse_str.pyx", line 10, in parse_str.load (parse_str.c:1460)

    L = loci.shape[1]

IndexError: tuple index out of range

-------------------------------------------------------------------------------------------

If any of you experienced this problem, I am interested in hearing how you solved it.

Thanks

V

[Vikram Chhatre]

One reason for this error is the presence of header in the data file, e.g. first row with names of loci.  This header should be removed for fastSTRUCTURE to work. 

V

[Simey]

Hi Vikram,

Yes, removing the first row with locus names fixed this issue. My input file was a Stacks populations output, which also includes a commented header that causes problem in both Structure and fastStructure. For e.g. 

# Stacks v1.20; Structure 2.3; August 12, 2014

this too must be removed from files generated by Stacks.

[xiaowei yang]

Thank you!
It works.

[aruna nandety]

Hi Vikram,

I am having the same problem. I have a text file from which I created an .str file. I left the first 4 columns empty, 5th column is individual ID, 6th column is population ID and then follows 3194 SNP marker data represented by 2 digits each. I left first row empty as suggested and then 372 individuals (2 rows per ID), but I still get the same error. I am pasting few rows and columns here.

1_1 1 22 11 11
1_1 1 22 22 11
1_10 1 11 11 22
1_10 1 22 11 22
1_11 1 11 22 22
1_11 1 22 22 22

$> python structure.py -K 2 --input=snp --format=str --output=out

Traceback (most recent call last):

File "structure.py", line 172, in <module>

G = parse_str.load(params['inputfile'])

File "parse_str.pyx", line 10, in parse_str.load (parse_str.c:1468)

L = loci.shape[1]
IndexError: tuple index out of range

Any help is highly appreciated. I am pretty sure that none of the individuals have 100% monomorphism.

Thank you
Aruna

[Alicia Talavera]

Hello, 

I have the same bug: 

Traceback (most recent call last):

  File "structure.py", line 172, in <module>

    G = parse_str.load(params['inputfile'])

  File "parse_str.pyx", line 10, in parse_str.load (parse_str.c:1455)

    L = loci.shape[1]

IndexError: tuple index out of range

And I have read: "One reason for this error is the presence of header in the data file, e.g. first row with names of loci.  This header should be removed for fastSTRUCTURE to work. "

But I haven't got header in my data file.

 Have you found another solution? 

Thank you!

[f.pina...@gmail.com]

Hello Alicia,

Can you please provide us with the command line you used that generated the error?

Also, take a look at your input file. Do you see anything obviously unusual? (such as lines with different lengths)
If all else fails, try a different input format (the error show you are using the "str" format, you can try using the "bed" format).

Francisco

[brian simison]

Another source of this error, for me, has been the coding for missing data. Stacks outputs "0" for missing data, FastStructure is looking for "-9". I use a simple awk command to convert "0" to "-9" (My samples have numbers in them):
cat populations.str | awk '{gsub(/\t0\t/,"\t-9\t");}1' > populationsFS.str

[Edgar Caballero]

Good morning faststructure commnunity I am new using the software in linux. I face the same problem as my  peers. I had an stacks populations structure format file which I edited on excel.  I Removed the comments headers row (#), loci headers row, added 4 columns with "#" and replaced "0" with  "-9".When I upload my file I transform it from txt to str format. Here I provide my commands :

structure.py -K $SGE_TASK_ID \

--input=/scratch/genomics/caballeroeg/FasSTRUCTURE/example_name \

--output=/scratch/genomics/caballeroeg/FasSTRUCTURE/K_$SGE_TASK_ID \

--tol=10e-6 \

--format=str \

--full

I have the same error as peers

My error: 

 Traceback (most recent call last):

File "/share/apps/bioinformatics/faststructure/conda/envs/faststructure/bin/structure.py", line 173, in <module>

G = parse_str.load(params['inputfile'])

File "parse_str.pyx", line 10, in parse_str.load

IndexError: tuple index out of range 

Given that the exmaples like headers or values does not apply here, what type of solution would you suggest to solve the problema

I would also like to ask if the output path refers a path to a folder, or an empty file (the empty file can be in .txt format?),

I would very much appreciate your advise and suggestions,

thanks in advance,

Edgar

[Edgar Caballero]

Hello Structure community

I solved it, it turns out that I created an extra row of "#" at the end of the .str file, I removed it and my analysis  ran well. I would recommend to check any malicious command or sintaxis error like this. Also I work in a linux environment so the endline command should be in LF or Linux. If you process an stacks output file after running populations I suggest copy the structure file with the extension .xls (in that way you can open it in excel) and modified the file. In excel I added the first 4 columns of "#", deleted the headers (including the ones with the names of the locis), and replaced the 0 with -9 .

I hope you guys can solve your issue.

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