multipop_selection_pipeline stopped at fst calculation #22
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Hi, thanks |
Hi Murray, Thanks for your quick reply. I tried that command and now it can finish the fst analysis and generate the following files: out.log out.windowed.weir.fst I am curious how to move forward from here because I am interested in applying this package to calculate different statistics like Tajima's D, Fay and Wu's H etc. for my own data. Thank you! |
The multi_selection_pipeline is actually just a wrapper for the selection_pipeline. I normally use selection_pipeline to run on single populations which generates Tajima's D, Fay Wu's H etc so that should hopefully work for you. Murray |
I've run into the same error when running I'm also getting the some weird error message after using the standalone
Is this due to some kind of compilation error during the installation process? It looks like I still get the 'out.windowed.weir.fst' file. Is there any output that should be there but is missing? When I run
Any idea how to address these items? Thanks! |
I am testing the multipop_selection_pipeline with the test lactase data. After running the following command, I noticed that it did not generate the Fst results and other files as described in the manual.
multipop_selection_pipeline -p CEU_ids.txt -p YRI_ids.txt -i CEU_YRI_lactase.vcf --config-file defaults.cfg -a "--imputation" -c 2 --imputation
The multi_population.log contains following info:
2017-06-28 12:01:54,452 fst_calculation_weir command = /software/selectiontools/1.0.1/bin/vcftools --fst-window-size 1000 --fst-window-step 1000 --vcf .../SelectionPipelineTestData/lactase/CEU_YRI_lactase.vcf --weir-fst-pop first_pop.tmp --weir-fst-pop second_pop.tmp
2017-06-28 12:01:54,699 fst_calculation_weir failed to run /software/selectiontools/1.0.1/bin/vcftools --fst-window-size 1000 --fst-window-step 1000 --vcf
.../SelectionPipelineTestData/lactase/CEU_YRI_lactase.vcf --weir-fst-pop first_pop.tmp --weir-fst-pop second_pop.tmp
The fst directory contains the following files:
first_pop.tmp second_pop.tmp stderr.tmp stdout.tmp
Is there any something else I should try?
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