Closed tommydavies closed 1 year ago
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.
This was posted in the wrong place - the error code belongs to a different software. Please ignore this issue.
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