can't limit to specific chromosome?

[h-orias]

Hi,

I'm attempting to run the tool on a specific chromosome using the --chroms arg. My command looks like such:

python //file.bam //file.fa //output-prefix --loci //file.bed --chroms 19 --debug --trf_args 2 7 7 80 10 50 500

I've tried running this both with "--chroms 19" and "--chroms chr19," but either way, the scan seems to start at chr1, which seems like a waste of resources. Please advise. Thanks for making this!

[readmanchiu]

If you are doing a scan, please don't supply the loci (--loci). Giving the loci bed file tells Straglr to go to genotype the loci instead of doing a genome scan on the chromosome(s).

[h-orias]

I understand, thank you. The new issue is that it returns "cannot run trf /tmp/tmpw4zwr89r.fa 2 5 5 80 10 10 500 -d -h". the command now looks like such:

python straglr.py //.bam //.fa //output-prefix --regions //PBMC_1316_chr19region.bed --debug

any thoughts?

[readmanchiu]

do you have trf installed in your PATH?

[h-orias]

was able to fix the trf hangup and have been successfully outputting files. the new question is whether i've installed blastn correctly: i downloaded the appropriate version of blastn and gunzipped the filed into my PATH, but i'm not sure if i have it done properly. currently I have the whole ncbi-blast-2.16.0+ folder in my bin, and the script throws this error:
blastn -query /tmp/tmpnlnfddr8.fa -subject /tmp/tmpzxb0qiso.fa -task blastn -word_size 4 -outfmt 6 -perc_identity 80 -qcov_hsp_perc 80 -out /tmp/tmpsnkwjs5v.blastn warning:cannot run blastn -query /tmp/tmpnlnfddr8.fa -subject /tmp/tmpzxb0qiso.fa -task blastn -word_size 4 -outfmt 6 -perc_identity 80 -qcov_hsp_perc 80 -out /tmp/ at the start of each run (but still successfully outputs .tsv, .bed, .vcf). which part of the blastn directory should I have in my PATH? thanks again.

[readmanchiu]

just the blastn binary is needed. You want the directory where the blastn binary resides in your path.
For example, if the path of your blastn binary is "/my/path/ncbi-blast-2.16.0/bin/blastn" then "/my/path/ncbi-blast-2.16.0/bin" should be in your PATH variable. If not, you can append in the your PATH in your .bashrc file:
export PATH=$PATH:/my/path/ncbi-blast-2.16.0/bin
You can then check if the os is able locate the binary by typing which blastn