jessiewu/bacterialgwas

A pipeline for performing genome-wide association tests for bacterial genomes.

bacterialgwas's Issues

cfml error

Hi Jessie-

When running the tri/tetra code, I get this error:

/Users/gotero/pertussis/gwasBacteria/CA_WA_snps_default.snpinfo.txt
/Users/gotero/pertussis/gwasBacteria/CA_WA_snps_default.snp.patterns.txt
/Users/gotero/pertussis/gwasBacteria/CA_WA_snps_default.snp.annotation.txt
Read 1 item
Read 298 items
Done 100
Error in cfml[position, ] : subscript out of bounds
Execution halted
flag3

Suggestions on what might be causing it? This is from an earlier version of the code.

Thanks!

Glen

Multiple correction

Output a suggested (-log10)P-value cutoff after correcting for multiple correction

Allow externalSoftware input file to vary for different command line specifications

Certain external software might not be required depending on the command line input. For example, RAxML or PhyML would not be required if the user provides a phylogenetic tree.

No such file .snp.annotation.txt

The Main program seems to expect a .snp.annotation.txt file to be present after running the getAnnotationsTritetraR script. But that script seems to produce a ttr.annotation.txt file. I'll create a PR with a fix for this.

typo in Usage Example, panGWAS_user_manual.pdf

Hi!

There is a typo in the panGWAS_user_manual.pdf, unfortunately in the Usage Example ;)

Rscript /path/of/make_pangenome.r –contigFile contigs.txt –prodigal yes – similarity 0.7 –coverage 0.7 –prefix test –externaSoftwarePaths soft.txt

externaSoftwarePaths should be changed to externalSoftwarePaths

Best wishes,

Kaisa

Kmer relatedness matrix

Enable calculations of the relatedness matrix directly from kmers.

Missing Script

Where is do_logreg_chw.R script?

SNP_GWAS_MAIN.R won't read the –script_dir parameter

The following command:

$ Rscript ~/installer/bacterialGWAS/snpGWAS/SNP_GWAS_MAIN.R -dataFile dataFile.tsv -externalSoftware externalSoftware.tsv -ref_fa example.2.fasta -ref_gbk example.2.gbk -prefix test03 –script_dir ~/installer/bacterialGWAS/snpGWAS/ 

Will return an error, as if the -script_dir parameter doesn't exist:

Start reading command inputs ...
1: -dataFile, 1
2: -externalSoftware, 1
3: -ref_fa, 1
4: -ref_gbk, 1
5: -prefix, 1
6: –script_dir, -1
Error in getCommandLineInputMatrix(args = args) : 
  Argument names must start with '-'! E.g. -phylogeny.
Execution halted