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GCP Life Sciences Discuss

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Welcome to gcp-life-sciences-discuss! We talk about life sciences projects led by the teams at Google Cloud & Google Brain:

https://cloud.google.com/life-sciences

https://github.com/googlegenomics/

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11/3/22

failed to execute google.cloud.lifesciences.v2beta.WorkflowsServiceV2Beta.RunPipeline

Hi everyone! I'm new on GoogleCloud and i ran gatk-sv pipeline trough Cromwell and PAPIv2 server

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failed to execute google.cloud.lifesciences.v2beta.WorkflowsServiceV2Beta.RunPipeline

Hi everyone! I'm new on GoogleCloud and i ran gatk-sv pipeline trough Cromwell and PAPIv2 server

11/3/22

Sheila Reynolds

4/6/22

anyone seen this "failed precondition" error before from a dsub run?

Failed precondition (HTTP 400): Execution failed: generic::failed_precondition: while running "

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anyone seen this "failed precondition" error before from a dsub run?

Failed precondition (HTTP 400): Execution failed: generic::failed_precondition: while running "

4/6/22

Josh, … Paul Grosu6

12/13/21

Query regarding gnomAD dataset on Bigquery

Hi Bashir, Great questions, and hope your are doing well! So let me answer both questions: 1)

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Query regarding gnomAD dataset on Bigquery

Hi Bashir, Great questions, and hope your are doing well! So let me answer both questions: 1)

12/13/21

Sheila Reynolds, … Paul Grosu13

11/2/21

current status of "dsub" ?

Hi Sheila, Matt is exactly right! Basically those (dsub/pipelines vs TES) are two different worlds.

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current status of "dsub" ?

Hi Sheila, Matt is exactly right! Basically those (dsub/pipelines vs TES) are two different worlds.

11/2/21

hze...@gmail.com, Randi Cowin2

8/30/21

Variant Transforms working , Big query generated table consisting of 2924 rows of 30 VCF files

Hi Aaron, Variant Transforms is a tool that uses a predefined ETL transformation to load variant call

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Variant Transforms working , Big query generated table consisting of 2924 rows of 30 VCF files

Hi Aaron, Variant Transforms is a tool that uses a predefined ETL transformation to load variant call

8/30/21

hze...@gmail.com

8/28/21

variant transforms interpretation

Dear Cloud life sciences team I want to know the working of Variant Transforms what I did I run 30

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variant transforms interpretation

Dear Cloud life sciences team I want to know the working of Variant Transforms what I did I run 30

8/28/21

Glen Beane, … Aaron Golden9

7/8/21

GCP Life Sciences API Pipeline "dockerCacheImages"

Hi Glen, Due to some issues last week and this week, the fix Tim mentioned above was not rolled out

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GCP Life Sciences API Pipeline "dockerCacheImages"

Hi Glen, Due to some issues last week and this week, the fix Tim mentioned above was not rolled out

7/8/21

6/22/21

Snakemake stuck at localrule All

Hi everyone, I am running a test Snakemake pipeline on GCP with google-life-sciences. Each rule runs

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Snakemake stuck at localrule All

Hi everyone, I am running a test Snakemake pipeline on GCP with google-life-sciences. Each rule runs

6/22/21

Bob, Tim Jennison3

6/17/21

Singularity not compatible with GCP life sciences?

Hi Tim, Thank you for verifying this! Greetings, Bob On Thursday, 17 June 2021 at 17:06:33 UTC+2 tjen

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Singularity not compatible with GCP life sciences?

Hi Tim, Thank you for verifying this! Greetings, Bob On Thursday, 17 June 2021 at 17:06:33 UTC+2 tjen

6/17/21

Mick Watson, Paul Grosu10

5/14/21

Persistant SSL errors when using Snakemake with google life sciences executor

Hi Mick, Nice analysis! As I initially suspected it probably was a race condition. By the way if

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Persistant SSL errors when using Snakemake with google life sciences executor

Hi Mick, Nice analysis! As I initially suspected it probably was a race condition. By the way if

5/14/21

Stephan Sie, … Mick Watson7

5/11/21

can you allocate resources for Snakemake pipeline?

You control how many jobs get submitted (and therefore VMs created) using the --jobs flag snakemake

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can you allocate resources for Snakemake pipeline?

You control how many jobs get submitted (and therefore VMs created) using the --jobs flag snakemake

5/11/21

Ilya Chorny, … Paul Grosu4

5/7/21

State of the Lifesciences API

Hi Shamel, That is good news to hear. But do you think a more comprehensive solution in the life

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State of the Lifesciences API

Hi Shamel, That is good news to hear. But do you think a more comprehensive solution in the life

5/7/21

Saman Vaisipour

4/21/21

Re: Variant Transforms 403 Error

Hi Randi, Please follow these instructions and make sure you have enabled all the required APIs. Also

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Re: Variant Transforms 403 Error

Hi Randi, Please follow these instructions and make sure you have enabled all the required APIs. Also

4/21/21

hze...@gmail.com, Saman Vaisipour4

3/10/21

Is varaint transform create empty tables please help

Please see my reply inline below: On Wed, Mar 10, 2021 at 1:14 PM hze...@gmail.com <hzebite@gmail.

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Is varaint transform create empty tables please help

Please see my reply inline below: On Wed, Mar 10, 2021 at 1:14 PM hze...@gmail.com <hzebite@gmail.

3/10/21

hze...@gmail.com, Andrew Carroll2

2/24/21

DEEP VARIANT RETURNS ERROR PLZHELP

Hi Haroon, First, the commands that you are using --noparse_sam_aux_fields --norealign_reads are

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DEEP VARIANT RETURNS ERROR PLZHELP

Hi Haroon, First, the commands that you are using --noparse_sam_aux_fields --norealign_reads are

2/24/21

hze...@gmail.com

2/24/21

Deep variant team can help

dear life sciences team i have run deep variant and its output directory generates following files

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Deep variant team can help

dear life sciences team i have run deep variant and its output directory generates following files

2/24/21

hze...@gmail.com, Paul Grosu2

2/14/21

here is the case of deepvariant

Hi Haroon, Remember my post from a month ago here regarding how to transfer files -- below is a link

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here is the case of deepvariant

Hi Haroon, Remember my post from a month ago here regarding how to transfer files -- below is a link

2/14/21

hze...@gmail.com2

2/13/21

Deep variant generated report.html file how to view in gcp ubuntu environment via google vhrome

---------- Forwarded message --------- From: hze...@gmail.com <Unknown> Date: Sunday, February

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Deep variant generated report.html file how to view in gcp ubuntu environment via google vhrome

---------- Forwarded message --------- From: hze...@gmail.com <Unknown> Date: Sunday, February

2/13/21

hze...@gmail.com, Andrew Carroll3

2/13/21

Deep variant can be used to analyze viral sequences or simply viruses or RNA

Hello Haroon, Thank you for your question. DeepVariant was developed with diploid variant calling in

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Deep variant can be used to analyze viral sequences or simply viruses or RNA

Hello Haroon, Thank you for your question. DeepVariant was developed with diploid variant calling in

2/13/21

hze...@gmail.com, Saman Vaisipour2

2/1/21

Variant Transforms returns same bug please resolve

Hi Haroon, You need to update your command as follows: COMMAND="vcf_to_bq \ --input_pattern ${

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Variant Transforms returns same bug please resolve

Hi Haroon, You need to update your command as follows: COMMAND="vcf_to_bq \ --input_pattern ${

2/1/21

Haroon Zeb, Saman Vaisipour2

2/1/21

Variant transforms returns bug while running preprocessor algorithm

Hi Haroon, You need to update your command as follows: COMMAND="vcf_to_bq_preprocess \ --

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Variant transforms returns bug while running preprocessor algorithm

Hi Haroon, You need to update your command as follows: COMMAND="vcf_to_bq_preprocess \ --

2/1/21

hze...@gmail.com, Paul Grosu2

1/20/21

can Variant Transforms work well on any variant caller format(vcf) file or particular vcf file?

Hi Haroon, Maybe you could please provide elaborations to the following two questions regarding

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can Variant Transforms work well on any variant caller format(vcf) file or particular vcf file?

Hi Haroon, Maybe you could please provide elaborations to the following two questions regarding

1/20/21

hze...@gmail.com, … Saman Vaisipour3

1/18/21

cloud storage bucket error when handing vcf files of large size outside gcp(when uploading from pc).variant transforms and deep variant

i am facing issues when uploading vcf files size of 1 gb or 2gb outside the GCP, it returns error

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cloud storage bucket error when handing vcf files of large size outside gcp(when uploading from pc).variant transforms and deep variant

i am facing issues when uploading vcf files size of 1 gb or 2gb outside the GCP, it returns error

1/18/21

Tim Jennison, … Paul Grosu8

12/11/20

Deprecation of the VirtualMachine.nvidia_driver_version field

And Matt, if you are experiencing issues among versions of Nvidia drivers, just post them here and we

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Deprecation of the VirtualMachine.nvidia_driver_version field

And Matt, if you are experiencing issues among versions of Nvidia drivers, just post them here and we

12/11/20

jam...@broadinstitute.org, … Tim Jennison4

12/4/20

Resource exhaustion despite OK quota, and retry frequency settings

Thank you, Tim. That is super helpful. I'll start by specifying zones instead of regions. Best,

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Resource exhaustion despite OK quota, and retry frequency settings

Thank you, Tim. That is super helpful. I'll start by specifying zones instead of regions. Best,

12/4/20

9/23/20

<LAUNCHED> GCP Variant Transforms Python 3 Migration

We're excited to announce that GCP Variant Transforms OSS tool has been migrated to Python 3 in

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<LAUNCHED> GCP Variant Transforms Python 3 Migration

We're excited to announce that GCP Variant Transforms OSS tool has been migrated to Python 3 in

9/23/20

mmun...@gmail.com, Saman Vaisipour3

9/2/20

Python 3 support for Variant Transforms

Saman, thanks for the quick response. I haven't run across any missing features yet. Just working

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Python 3 support for Variant Transforms

Saman, thanks for the quick response. I haven't run across any missing features yet. Just working

9/2/20

8/17/20

Service Account Creation Change Announcement

An upcoming change to the Life Sciences API will result in the Life Sciences service account being

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Service Account Creation Change Announcement

An upcoming change to the Life Sciences API will result in the Life Sciences service account being

8/17/20

Tim Jennison, mboo...@google.com3

8/5/20

Metadata TTL change in Genomics v2alpha1

Hi Matt, Yes, that would be sufficient to capture all operation metadata. Note that it may take a

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Metadata TTL change in Genomics v2alpha1

Hi Matt, Yes, that would be sufficient to capture all operation metadata. Note that it may take a

8/5/20

sam...@google.com, joseph...@providence.org2

7/10/20

Variant Transforms v0.9.0 is released

Congrats. Glad to see the new version! On Thursday, July 9, 2020 at 7:25:57 PM UTC-4 sam...@google.

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Variant Transforms v0.9.0 is released

Congrats. Glad to see the new version! On Thursday, July 9, 2020 at 7:25:57 PM UTC-4 sam...@google.

7/10/20

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