kmers_gwas.py cannot find a pheno.phenotypes_and_permutations file

[tommydavies]

Hi there,

I am running the kmers_gwas.py script:

sudo python2.7 /kmers_gwas.py --pheno phenotype.pheno --kmers_table kmers_table -l 31 -p 8 --outdir kmer_results

This throws the following error: Traceback (most recent call last): File "//src/py/align_kinship_phenotype.py", line 83, in main() File "//src/py/align_kinship_phenotype.py", line 56, in main phenotype_val = get_column(args.fn_phenotype, 1)[1:] # Phenotypes values File "/src/py/functions.py", line 14, in get_column return [line.split(sep)[index] for line in file(fn,"r").read().split("\n")[:-1]] IndexError: list index out of range sh: 1: Rscript: not found Traceback (most recent call last): File "/kmers_gwas.py", line 278, in main() File "/kmers_gwas.py", line 107, in main phenotypes_names = file(paths["pheno_permuted_fn"] ,"r").read().split("\n")[0].split("\t")[1:]

IOError: [Errno 2] No such file or directory: 'kmer_results/pheno.phenotypes_and_permutations'

The manual does not mention any generation of such a file. Is there something I am missing?

I have tried with phenotype data with NA's as well as without NA's.

Please let me know why I might be getting this error.

Thanks, Tommy

[tommydavies]

Hi all. If you experience the above error, check that your phenotype table does not have an extra newline (\n) at the end. It will produce the above error.

[tommydavies]

This was posted in the wrong place - the error code belongs to a different software. Please ignore this issue.