Search

Clear search

Close search

Main menu

Google apps

Cumulus Support

Contact owners and managers

1–30 of 109

0 selected

Mar 13

Re: Error in generating UMI count plot

Hi Laura, This error usually indicates that the generated count matrix does not capture any valid

unread,

Re: Error in generating UMI count plot

Hi Laura, This error usually indicates that the generated count matrix does not capture any valid

Mar 13

Laura Drepanos, Yiming Yang2

Mar 8

cellranger_workflow seeming to be incompatible with Cellranger 8.0.0+?

Hello Laura, May I know which workflow version you are using? From your issue with "--create-bam

unread,

cellranger_workflow seeming to be incompatible with Cellranger 8.0.0+?

Hello Laura, May I know which workflow version you are using? From your issue with "--create-bam

Mar 8

Mar 8

Cumulus 3.0.0 is released

Hello All, Cumulus version 3.0.0 is released. The release notes can be viewed at https://github.com/

unread,

Cumulus 3.0.0 is released

Hello All, Cumulus version 3.0.0 is released. The release notes can be viewed at https://github.com/

Mar 8

Adam Rubin, Yiming Yang2

Mar 6

Cellranger error from strato --backend flag

Hello Adam, Sorry for this inconvenience. The issue is because the mkfastq step uses an internal

unread,

Cellranger error from strato --backend flag

Hello Adam, Sorry for this inconvenience. The issue is because the mkfastq step uses an internal

Mar 6

Mar 6

Re: No space left on device error

Hi Laura, You can increase the disk space for your adt job by specifying "feature_disk_space

unread,

Re: No space left on device error

Hi Laura, You can increase the disk space for your adt job by specifying "feature_disk_space

Mar 6

Francesco Corrado, Yiming Yang2

Mar 6

Cellranger annotate

Hello Francesco, It seems this cellranger annotate feature requires having Cloud token from 10x cloud

unread,

Cellranger annotate

Hello Francesco, It seems this cellranger annotate feature requires having Cloud token from 10x cloud

Mar 6

Julien Dilly, … Yiming Yang5

9/10/24

Terra CellRanger | Docker access permission denied

Just include Deeptha from Broad into this email thread. Hi Deeptha, As you can read from the quoted

unread,

Terra CellRanger | Docker access permission denied

Just include Deeptha from Broad into this email thread. Hi Deeptha, As you can read from the quoted

9/10/24

8/2/24

Cumulus 2.6.3 is released

Hello All, Cumulus version 2.6.3 is released. This is a small bug-fix release. The release notes can

unread,

Cumulus 2.6.3 is released

Hello All, Cumulus version 2.6.3 is released. This is a small bug-fix release. The release notes can

8/2/24

Francesco Corrado, Yiming Yang3

7/4/24

Workflow error- Cellranger count

Hi Yiming thank you so much for your support!! Now it is working, I will let you know if I have other

unread,

Workflow error- Cellranger count

Hi Yiming thank you so much for your support!! Now it is working, I will let you know if I have other

7/4/24

Andrew Navia, Yiming Yang2

6/28/24

Multiplexed FRP on cellranger_multi

Hi Andrew, It looks like this GitHub issue is yours: https://github.com/lilab-bcb/cumulus/issues/406.

unread,

Multiplexed FRP on cellranger_multi

Hi Andrew, It looks like this GitHub issue is yours: https://github.com/lilab-bcb/cumulus/issues/406.

6/28/24

6/19/24

Cumulus 2.6.2 is released

Hello All, Cumulus version 2.6.2 is released. The release notes can be viewed at https://github.com/

unread,

Cumulus 2.6.2 is released

Hello All, Cumulus version 2.6.2 is released. The release notes can be viewed at https://github.com/

6/19/24

6/12/24

Pegasus 1.10.0 is released

Hello All, Pegasus version 1.10.0 is released, along with PegasusIO version 0.9.1. The new features

unread,

Pegasus 1.10.0 is released

Hello All, Pegasus version 1.10.0 is released, along with PegasusIO version 0.9.1. The new features

6/12/24

5/8/24

Cumulus 2.6.1 is released

Hello All, Cumulus version 2.6.1 is released. The release notes can be viewed at https://github.com/

unread,

Cumulus 2.6.1 is released

Hello All, Cumulus version 2.6.1 is released. The release notes can be viewed at https://github.com/

5/8/24

David Lieb, Yiming Yang3

5/3/24

Can't access Cellranger 8.0.0

Hi Yiming, Thanks for your quick response. I tried the workflow for count with the default Cellranger

unread,

Can't access Cellranger 8.0.0

Hi Yiming, Thanks for your quick response. I tried the workflow for count with the default Cellranger

5/3/24

4/22/24

Cumulus 2.6.0 is released

Hello All, Cumulus version 2.6.0 is released. The release notes can be viewed at https://github.com/

unread,

Cumulus 2.6.0 is released

Hello All, Cumulus version 2.6.0 is released. The release notes can be viewed at https://github.com/

4/22/24

Yuan Lian, Yiming Yang4

4/10/24

Re: workflow error

Thank you for your help Yiming! It works now. Best, Ansel On Tue, Apr 9, 2024 at 5:26 PM Yiming Yang

unread,

Re: workflow error

Thank you for your help Yiming! It works now. Best, Ansel On Tue, Apr 9, 2024 at 5:26 PM Yiming Yang

4/10/24

2/27/24

STARSolo Error: Parsing problem

Hello, I am running into issues when trying to use STARsolo imported to Terra via Dockstore. It seems

unread,

STARSolo Error: Parsing problem

Hello, I am running into issues when trying to use STARsolo imported to Terra via Dockstore. It seems

2/27/24

Laura Domenech, Yiming Yang4

2/26/24

Demultiplexing 2.5 errors

Hello, Just a Demuxlet update: still running with one pool of 2 samples (running time 22h), and still

unread,

Demultiplexing 2.5 errors

Hello, Just a Demuxlet update: still running with one pool of 2 samples (running time 22h), and still

2/26/24

2/3/24

Cumulus 2.5.0 is released

Hello All, Cumulus version 2.5.0 is released. The release notes can be viewed at https://github.com/

unread,

Cumulus 2.5.0 is released

Hello All, Cumulus version 2.5.0 is released. The release notes can be viewed at https://github.com/

2/3/24

David Lieb, Yiming Yang2

1/21/24

Error running Smart-Seq2 workflow on Terra

Hi David, Hope this email finds you well. The issue on missing stratocumulus package has been fixed

unread,

Error running Smart-Seq2 workflow on Terra

Hi David, Hope this email finds you well. The issue on missing stratocumulus package has been fixed

1/21/24

1/21/24

Pegasus 1.9.0 is released

Hello All, Pegasus version 1.9.0 is released, along with PegasusIO version 0.9.0. The new features

unread,

Pegasus 1.9.0 is released

Hello All, Pegasus version 1.9.0 is released, along with PegasusIO version 0.9.0. The new features

1/21/24

Hanna Schumacher

10/18/23

Difference to AnnData?

Hello all, I just discovered Pegasus and am now wondering, what the difference to an AnnData object

unread,

Difference to AnnData?

Hello all, I just discovered Pegasus and am now wondering, what the difference to an AnnData object

10/18/23

Christopher Dall

10/17/23

Trouble with cumulus cellranger count on terra

Hi all, Very new to terra and cellranger, so I will try to provide as much information as possible. I

unread,

Trouble with cumulus cellranger count on terra

Hi all, Very new to terra and cellranger, so I will try to provide as much information as possible. I

10/17/23

Alyssa DuBois, Yiming Yang2

10/12/23

Cumulus ADT adding spaces to file names

Hello Alyssa, Thanks for reaching! May I know the version of Cumulus cellranger workflow that you

unread,

Cumulus ADT adding spaces to file names

Hello Alyssa, Thanks for reaching! May I know the version of Cumulus cellranger workflow that you

10/12/23

dina...@student.ubc.ca, Yiming Yang6

8/26/23

Pegasus human_lung Marker set Issue Inquiry

Dear Dina, Glad it works finally. And thank you very much for reporting these issues to help us

unread,

Pegasus human_lung Marker set Issue Inquiry

Dear Dina, Glad it works finally. And thank you very much for reporting these issues to help us

8/26/23

Rodrigo Martinez Maza, Yiming Yang2

6/26/23

cell ranger_count workflow error

Hello Rodrigo, Can you send me the "generate_count_config.log" file in the execution folder

unread,

cell ranger_count workflow error

Hello Rodrigo, Can you send me the "generate_count_config.log" file in the execution folder

6/26/23

He, Yiwen, Bo Li2

5/29/23

Pegasus installation issues for macOS

Hi Yiming, Can you take a look when you have time? Thanks, Bo Bo Li, Ph.D. Principal Scientist,

unread,

Pegasus installation issues for macOS

Hi Yiming, Can you take a look when you have time? Thanks, Bo Bo Li, Ph.D. Principal Scientist,

5/29/23

4/18/23

Re: help with setting cirrocumulus

Hi Sisi, The localhost approach is used for self-viewing the data interactively without downloading.

unread,

Re: help with setting cirrocumulus

Hi Sisi, The localhost approach is used for self-viewing the data interactively without downloading.

4/18/23

3/22/23

Cumulus on Terra

Hello, I am new to using the Cumulus workflow on Terra and just getting familiar. I am looking to see

unread,

Cumulus on Terra

Hello, I am new to using the Cumulus workflow on Terra and just getting familiar. I am looking to see

3/22/23

Monika Looney, Yiming Yang6

3/14/23

bcl2fastq docker image

Please see my inline comments below. On Mon, Mar 13, 2023 at 11:56 PM Monika Looney <monika.looney

unread,

bcl2fastq docker image

Please see my inline comments below. On Mon, Mar 13, 2023 at 11:56 PM Monika Looney <monika.looney

3/14/23