IOError: [Errno 2] No such file or directory

[Alicia Talavera]

Hello, 

I write this email because I would like to use faststructure, but I obtain all the time this bug: 

Traceback (most recent call last):

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

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

  File "parse_str.pyx", line 7, in parse_str.load (parse_str.c:1292)

    handle = open(file+'.str','r')

IOError: [Errno 2] No such file or directory: 'prueba_faststructure01.str'

Could you help me? Below I specify everything. 

The script I ran was: 

python structure.py -K 2 --input=prueba_faststructure01 --output=/data/prueba/fastStructure/outputfaststructure/prueba_faststructure01_output --format=str 

My input was in the same directory than structure.py. and was created using PDGSpider from my VCF file to structure format . I selected yes in the question: save more specific fast structure format?. 

Also, I have read :  "2. Use pgdSpider to convert from vcf to structure or faststructure. Make sure to run --maf filter in vcftools prior to converting the files, to get rid of any monomorphic loci.  The --min-alleles and --max-alleles, even when both set at a value of 2 do not get rid of monomorphic sites.  The --maf filter (keep it very low) will accomplish this.  If monomorphic sites are retained, pgdSpider is unable to properly convert the data.". So I have tried to run this script before to run fast-structure : 

vcftools --vcf myfile.vcf --maf 0.02 --recode --recode-INFO-all --out myinputfast.vcf

But I obtain the same bug. 

Could you help me? I am stuck. 

Thank you!!

[Vikram Chhatre]

Please post the output of this command in your working directory: 

$ ls -lh

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