search

genepi / imputationserver-docker

Docker Image for Michigan Imputation Server
18 stars 13 forks source link

Can't progress Imputation for Chr X #7

Open innerpyg-bi opened 4 years ago

innerpyg-bi commented 4 years ago

I analyzed by following steps.

1. docker run -d -p 4000 genepi/imputationserver:v1.2.7 2. access http://localhost:4000 3. install 1000genomes-phase3 reference panel in Admin Panel

4. local download and make m3vcf and bcf files for Chr X 5. Insert the m3vcf and bcf file into /data/apps/1000g-phase-3-v5/2.0.0 on genepi/imputationserver:v1.2.7 6. docker exec -t -i ImputationServer cloudgene run imputationserver@1.2.7 --files /mnt/$PWD/nonPAR.vcf.gz --refpanel apps@1000g-phase-3-v5@2.0.0 --conf /etc/hadoop/conf --population eas &> docker.log

In this case, I can see this log. MI_nonPAR_Error

Please let me know how to fix Thanks

seppinho commented 4 years ago

Can you try the same file on https://imputationserver.sph.umich.edu?

innerpyg-bi commented 4 years ago

Today, I analyzed web based imputation server using same file. Chr22 vcf file was finished. but not ChrX.

seppinho commented 4 years ago

thanks for testing. any chances you can share a test file that fails?

innerpyg-bi commented 4 years ago

I'm sending you a vcf file with only the sample ID changed. nonPAR_Update.vcf.gz

Thank you for your concern.

seppinho commented 4 years ago

Had to unzip/bgzip it again but worked then on the server. Can you please double check? nonPAR_Update.vcf.gz

innerpyg-bi commented 4 years ago

Oh, i found when doesn't work on web. When i select the reference panel which is EUR and Other/Mixed poputation of 1000G Phase3 V5 hg19, it works but not the others. I also checked on docker, but still doesn't work including eur.

o147942 commented 4 years ago

I cannot find the bcf file of the chrX in bcfs folder in hapmap and 1000g reference panel of docker. Why there is no chrX file?