multipop_selection_pipeline run error #25
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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 |
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
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Department of Biochemsitry,
CONAS, Makerere University
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Hi Julius, I think github has stripped the attachment. 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.
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 |
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?
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