allow configuration file to have resources per instrument type #106
Assignees
Comments
|
It might also be worth looking at the flow cell type since diff flow cells on same instrument have very different output
… On Oct 10, 2023, at 11:40 AM, Antonio Gonzalez ***@***.***> wrote:
iSeq processing uses way less resources than NovaSeq so it will be good to account for this while generating the compute resource allocations. In other words, we should allow for specific requests for iSeq via the config file.
Now, to id the instrument type, we need to use the letter after the first underscore in the runid; (from Gail) """e.g. 231005_A01535_0399_BHFNWNDSX7 where A01535 is the number of the instrument 01535, and A means NovaSeq
For: 20231009_FS10001773_73_BTR67718-2515, FS dentes iSeq and 0001773 is the machine number."""
—
Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/biocore/mg-scripts/issues/106__;!!Mih3wA!EEloVeS6npQOXUJpQqJ_MANpKv20eN10gvokKUE9wP1uXYtaobgKanzHNHB1lertLdD-ofB89qcgLTySQWPhn_ehyw$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AAPL2KIRJHTT2ZOMSCDXL23X6WJCNAVCNFSM6AAAAAA52ZR6V2VHI2DSMVQWIX3LMV43ASLTON2WKOZRHEZTKOJYGE4DAMQ__;!!Mih3wA!EEloVeS6npQOXUJpQqJ_MANpKv20eN10gvokKUE9wP1uXYtaobgKanzHNHB1lertLdD-ofB89qcgLTySQWMZbx4HlA$>.
You are receiving this because you are subscribed to this thread.
|
|
@rob-knight; after discussing the flow cell suggestion with Gail, we realized that flow cell type is not something currently being tracked but based on the machine id, it can be inferred. |
|
Looks like this info can be harvested from the xmls. I'm guessing the field is (qiime2-2023.5) 13:31:14 (dtmcdonald@barnacle2):2023.10.10-gencode-v44$ grep -i flow /sequencing/igm_runs/231005_A01535_0399_BHFNWNDSX7/RunInfo.xml
<Flowcell>HFNWNDSX7</Flowcell>
<FlowcellLayout LaneCount="4" SurfaceCount="2" SwathCount="6" TileCount="78" FlowcellSide="2">
</FlowcellLayout>
(qiime2-2023.5) 13:31:22 (dtmcdonald@barnacle2):2023.10.10-gencode-v44$ grep -i flow /sequencing/igm_runs/231005_A01535_0399_BHFNWNDSX7/RunParameters.xml
<FlowCellSerialBarcode>HFNWNDSX7</FlowCellSerialBarcode>
<FlowCellPartNumber>20015843</FlowCellPartNumber>
<FlowCellLotNumber>20747361</FlowCellLotNumber>
<FlowCellExpirationdate>04/13/2024 00:00:00</FlowCellExpirationdate>
<FlowCellStartDate>10/05/2023 18:20:00</FlowCellStartDate>
<FlowCellNumberOfReuseRemaining>1</FlowCellNumberOfReuseRemaining>
<FlowCellSupportedModes>HTWashOnly;S4</FlowCellSupportedModes>
<FlowCellMode>S4</FlowCellMode>
<FlowCellConsumableVersion>1</FlowCellConsumableVersion>
<FlowCellRssi>3</FlowCellRssi>
<Board>Flow Cell Holder Board</Board>
<WorkflowType>NovaSeqXp</WorkflowType> |
|
Correct, thanks for checking this!
… On Oct 10, 2023, at 1:33 PM, Daniel McDonald ***@***.***> wrote:
Looks like this info can be harvested from the xmls. I'm guessing the field is FlowCellMode (bolded below) but it would be good to confirm that, Kristin can likely verify quickly
(qiime2-2023.5) 13:31:14 ***@***.***):2023.10.10-gencode-v44$ grep -i flow /sequencing/igm_runs/231005_A01535_0399_BHFNWNDSX7/RunInfo.xml
<Flowcell>HFNWNDSX7</Flowcell>
<FlowcellLayout LaneCount="4" SurfaceCount="2" SwathCount="6" TileCount="78" FlowcellSide="2">
</FlowcellLayout>
(qiime2-2023.5) 13:31:22 ***@***.***):2023.10.10-gencode-v44$ grep -i flow /sequencing/igm_runs/231005_A01535_0399_BHFNWNDSX7/RunParameters.xml
<FlowCellSerialBarcode>HFNWNDSX7</FlowCellSerialBarcode>
<FlowCellPartNumber>20015843</FlowCellPartNumber>
<FlowCellLotNumber>20747361</FlowCellLotNumber>
<FlowCellExpirationdate>04/13/2024 00:00:00</FlowCellExpirationdate>
<FlowCellStartDate>10/05/2023 18:20:00</FlowCellStartDate>
<FlowCellNumberOfReuseRemaining>1</FlowCellNumberOfReuseRemaining>
<FlowCellSupportedModes>HTWashOnly;S4</FlowCellSupportedModes>
**<FlowCellMode>S4</FlowCellMode>**
<FlowCellConsumableVersion>1</FlowCellConsumableVersion>
<FlowCellRssi>3</FlowCellRssi>
<Board>Flow Cell Holder Board</Board>
<WorkflowType>NovaSeqXp</WorkflowType>
—
Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/biocore/mg-scripts/issues/106*issuecomment-1756185617__;Iw!!Mih3wA!Hzne3qzmA2tWwCjOgC3udb1-wh5ySPu0M40HHn8VtlbfSYNu-mcXWnG59yZqbVfxHSz5Rgmsnv1bAHTYO48iE6VfqQ$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AAPL2KN33RON427K2D54KQ3X6WWJFAVCNFSM6AAAAAA52ZR6V2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJWGE4DKNRRG4__;!!Mih3wA!Hzne3qzmA2tWwCjOgC3udb1-wh5ySPu0M40HHn8VtlbfSYNu-mcXWnG59yZqbVfxHSz5Rgmsnv1bAHTYO49UQVqxzg$>.
You are receiving this because you were mentioned.
|
|
just an FYI I skimmed through the RunParameters.xml files for different sections of the /sequencing mount on barnacle and I noticed that FlowCellMode only appears in runs under igm_runs. Do we anticipate needing this value for other iseq and other runs as well? |
Closed
|
I think Jeff or Gail will know more about that ... can you send them a email directly? Thank you. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
iSeq processing uses way less resources than NovaSeq so it will be good to account for this while generating the compute resource allocations. In other words, we should allow for specific requests for iSeq via the config file.
Now, to id the instrument type, we need to use the letter after the first underscore in the runid; (from Gail) """e.g. 231005_A01535_0399_BHFNWNDSX7 where A01535 is the number of the instrument 01535, and A means NovaSeq
For: 20231009_FS10001773_73_BTR67718-2515, FS dentes iSeq and 0001773 is the machine number."""
The text was updated successfully, but these errors were encountered: