multipop_selection_pipeline run error

[mujuls]

I am trying to run multipop_selection_pipeline on my data set and encountering the following error on executing the run:
--imputation
Traceback (most recent call last):
File "/usr/bin/multipop_selection_pipeline", line 9, in
load_entry_point('selectionTools==1.1.1', 'console_scripts', 'multipop_selection_pipeline')()
File "/usr/lib/python2.7/site-packages/selectionTools-1.1.1-py2.7.egg/selection_pipeline/multipipeline.py", line 369, in main
fst_vcf(options.vcf_input, config, options, populations)
File "/usr/lib/python2.7/site-packages/selectionTools-1.1.1-py2.7.egg/selection_pipeline/multipipeline.py", line 283, in fst_vcf
options.chromosome + p + s + '.weir.fst')
OSError: [Errno 2] No such file or directory

I am running it on Scientific Linux release 7.2 and the installation was successful.
Is there something I am missing?

[murraycadzow]

Hi,

My first point of call would be to look at the command being run and also the config file to make sure that something isn't missing

Could you post the command that was run and also the contents of your config file (most likely called defaults.cfg). The log file would also be useful

thanks
Murray

[mujuls]

Hi Murray, I would like to run the selection pipeline on populations in a merged file that contains 1000genome+Mydata, in a vcf.gz format. I used the multi population pipeline script below; attached is the log file which indicated the use of a .gz file rather than .vcf. However including --gzvcf in the script did not work. multipop_selection_pipeline -p UGN.txt -p UGB.txt \ -i /scratch/julius/vcf/Chr22.tgen_1kg_eth.filtered.recode.rehead.vcf.gz --config-file /scratch/julius/selection/selectionTools/defaults.cfg \ -a "--imputation" -c 22 Since you had indicated in a previous thread that you often run the selection pipeline on a single population, I tried it with the script below and again got the same error; selection_pipeline --population UGN.txt \ i /scratch/julius/vcf/Chr22.tgen_1kg_eth.filtered.recode.rehead.vcf.gz \ --haps /scratch/julius/phased/Chr22.tgen_1kg_eth.filtered.phase.haps \ --sample /scratch/julius/phased/Chr22.tgen_1kg_eth.filtered.phase.rehead.sample \ --config-file /scratch/julius/selection/selectionTools/defaults.cfg \ --imputation -c 22 Traceback (most recent call last): File "/usr/bin/selection_pipeline", line 9, in <module> load_entry_point('selectionTools==1.1.1', 'console_scripts', 'selection_pipeline')() File "/usr/lib/python2.7/site-packages/selectionTools-1.1.1-py2.7.egg/selection_pipeline/selection_pipeline.py", line 248, in main s.run_pipeline() File "/usr/lib/python2.7/site-packages/selectionTools-1.1.1-py2.7.egg/selection_pipeline/standard_run.py", line 241, in run_pipeline (haps) = self.run_impute2(haps) File "/usr/lib/python2.7/site-packages/selectionTools-1.1.1-py2.7.egg/selection_pipeline/standard_run.py", line 386, in run_impute2 haps) File "/usr/lib/python2.7/site-packages/selectionTools-1.1.1-py2.7.egg/selection_pipeline/run_pipeline.py", line 184, in run_impute2 "Hap file cannot be found for chromosome {0}".format(self.options.chromosome) AssertionError: Hap file cannot be found for chromosome 22 Attached please find the config file that I am using. Thank you for the prompt response. Kind regards, Julius

…

On Thu, Feb 22, 2018 at 1:59 AM, murraycadzow ***@***.***> wrote: Hi, My first point of call would be to look at the command being run and also the config file to make sure that something isn't missing Could you post the command that was run and also the contents of your config file (most likely called defaults.cfg). The log file would also be useful thanks Murray — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#25 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Ai_o8XMr1SUxs8Dfh69hTAzANyNqiELhks5tXJ--gaJpZM4SNT8n> .

-- Julius Mulindwa, PhD Department of Biochemsitry, CONAS, Makerere University

[murraycadzow]

Hi Julius,

I think github has stripped the attachment.
But I'll have a guess at a few of the options that might be cause this failing

first of all go to /scratch/julius/selection/selectionTools/bin (I'm assuming that's where you installed selection tools) and run shapeit (./shapeit --help) and impute2 (./impute2) and see if you get the help dialogue for shapeit, and a copyright notice for impute2.
If you don't get that output then you might need to download and install those programs - I haven't updated the install script in a while so the links it points to might no longer exist. To install I think you download and extract and then copy the shapeit/impute2 binary into the directory mentioned above.

• while you're in that directory also see if qctool (./qctool) runs

secondly, I see that you are trying to do imputation, if you imputing in humans, I would recommend using https://imputation.sanger.ac.uk or https://imputationserver.sph.umich.edu/index.html which are both free and are setup better than selection_tools is for imputation. If you use these services then I think using the phasing option of eagle will give you back a phased imputed vcf, otherwise if you use shapeit2 on these services you will need to phase the imputed vcf you get back. Or do the imputation first before using selection tools as there is no qc step implemented post imputation within the pipeline.

thirdly, you only need to specify either -i or --haps/--sample. if you use -i and the vcf is phased then you can add on --phased-vcf to skip the phasing step

hopefully that starts to solve the issue you're having