Nextflow with Azure Batch - 找不到匹配的 VM 映像
Nextflow with Azure Batch - Cannot find a matching VM image
尝试使用 Azure Batch (NF-Core) 设置 Nextflow 时,出现以下错误。我在多个工作流程(sarek、ataseq 等)上尝试过这个。我得到了同样的错误 -
N E X T F L O W ~ version 22.04.0
Pulling nf-core/atacseq ...
downloaded from https://github.com/nf-core/atacseq.git
Launching `https://github.com/nf-core/atacseq` [rhl6d5529] DSL1 - revision: 1b3a832db5 [1.2.1]
Downloading plugin nf-azure@0.13.1
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/atacseq v1.2.1
----------------------------------------------------
Run Name : rhl6d5529
Data Type : Paired-End
Design File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/design.csv
Genome : Not supplied
Fasta File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa
GTF File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf
Mitochondrial Contig : MT
MACS2 Genome Size : 1.2E+7
Min Consensus Reps : 1
MACS2 Narrow Peaks : No
MACS2 Broad Cutoff : 0.1
Trim R1 : 0 bp
Trim R2 : 0 bp
Trim 3' R1 : 0 bp
Trim 3' R2 : 0 bp
NextSeq Trim : 0 bp
Fingerprint Bins : 100
Save Genome Index : No
Max Resources : 6 GB memory, 2 cpus, 12h time per job
Container : docker - nfcore/atacseq:1.2.1
Output Dir : ./results
Launch Dir : /
Working Dir : /nextflow/atacseq/rhl6d5529
Script Dir : /.nextflow/assets/nf-core/atacseq
User : root
Config Profile : test,azurebatch
Config Description : Minimal test dataset to check pipeline function
Config Contact : Venkat Malladi (@vsmalladi)
Config URL : https://azure.microsoft.com/services/batch/
----------------------------------------------------
Uploading local `bin` scripts folder to az://nextflow/atacseq/rhl6d5529/tmp/66/bd55d79e42999df38ba04a81c3aa04/bin
[- ] process > CHECK_DESIGN -
[- ] process > CHECK_DESIGN [ 0%] 0 of 1
[- ] process > CHECK_DESIGN [ 0%] 0 of 1
Error executing process > 'CHECK_DESIGN (design.csv)'
Caused by:
Cannot find a matching VM image with publisher=microsoft-azure-batch; offer=centos-container; OS type=linux; verification type=verified
[58/55b7f7] process > CHECK_DESIGN (design.csv) [100%] 1 of 1, failed: 1
Error executing process > 'CHECK_DESIGN (design.csv)'
Caused by:
Cannot find a matching VM image with publisher=microsoft-azure-batch; offer=centos-container; OS type=linux; verification type=verified
我试着查看 nextflow 的源代码。我发现错误在 AzBatchService.groovy
(下面的行号)中。
我在我的 Azure Batch 帐户实例中做了一些进一步的挖掘。基本上,我想确认从 Azure Batch 帐户收到的支持图像列表是否包含此管道所需的图像。我可以确认服务器确实响应了所需的图像 -
这可能是什么问题?我记得几周前 运行 完全相同的管道,它确实工作了几次。我错过了什么吗?
刚刚又看了一遍 Azure Cloud 文档,认为这可能是相关的:
By default, Nextflow creates CentOS 8-based pool nodes, but this
behavior can be customised in the pool configuration. Below the
configurations for image reference/SKU combinations to select two
popular systems.
- Ubuntu 20.04:
sku = "batch.node.ubuntu 20.04"
offer = "ubuntu-server-container"
publisher = "microsoft-azure-batch"
- CentOS 8 (default):
sku = "batch.node.centos 8"
offer = "centos-container"
publisher = "microsoft-azure-batch"
我认为这里的问题是不匹配 nodeAgentSkuId
。 Nextflow 期望 CentOS 8 节点代理 SKU,但您有 CentOS 7 SKU。如果无法以某种方式更改 nodeAgentSkuId
,Nextflow 使用的节点代理 SKU 应该可以通过将其添加到您的 nextflow.config
:
来覆盖
azure.batch.pools.<name>.sku = 'batch.node.centos 7'
其中 <name>
是池标识符:
azure.batch.pools.<name>.sku
Specify the ID of the Compute Node agent SKU which the pool identified with <name>
supports (default: batch.node.centos 8
, requires nf-azure@0.11.0
).
https://www.nextflow.io/docs/edge/azure.html#advanced-settings
尝试使用 Azure Batch (NF-Core) 设置 Nextflow 时,出现以下错误。我在多个工作流程(sarek、ataseq 等)上尝试过这个。我得到了同样的错误 -
N E X T F L O W ~ version 22.04.0
Pulling nf-core/atacseq ...
downloaded from https://github.com/nf-core/atacseq.git
Launching `https://github.com/nf-core/atacseq` [rhl6d5529] DSL1 - revision: 1b3a832db5 [1.2.1]
Downloading plugin nf-azure@0.13.1
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/atacseq v1.2.1
----------------------------------------------------
Run Name : rhl6d5529
Data Type : Paired-End
Design File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/design.csv
Genome : Not supplied
Fasta File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa
GTF File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf
Mitochondrial Contig : MT
MACS2 Genome Size : 1.2E+7
Min Consensus Reps : 1
MACS2 Narrow Peaks : No
MACS2 Broad Cutoff : 0.1
Trim R1 : 0 bp
Trim R2 : 0 bp
Trim 3' R1 : 0 bp
Trim 3' R2 : 0 bp
NextSeq Trim : 0 bp
Fingerprint Bins : 100
Save Genome Index : No
Max Resources : 6 GB memory, 2 cpus, 12h time per job
Container : docker - nfcore/atacseq:1.2.1
Output Dir : ./results
Launch Dir : /
Working Dir : /nextflow/atacseq/rhl6d5529
Script Dir : /.nextflow/assets/nf-core/atacseq
User : root
Config Profile : test,azurebatch
Config Description : Minimal test dataset to check pipeline function
Config Contact : Venkat Malladi (@vsmalladi)
Config URL : https://azure.microsoft.com/services/batch/
----------------------------------------------------
Uploading local `bin` scripts folder to az://nextflow/atacseq/rhl6d5529/tmp/66/bd55d79e42999df38ba04a81c3aa04/bin
[- ] process > CHECK_DESIGN -
[- ] process > CHECK_DESIGN [ 0%] 0 of 1
[- ] process > CHECK_DESIGN [ 0%] 0 of 1
Error executing process > 'CHECK_DESIGN (design.csv)'
Caused by:
Cannot find a matching VM image with publisher=microsoft-azure-batch; offer=centos-container; OS type=linux; verification type=verified
[58/55b7f7] process > CHECK_DESIGN (design.csv) [100%] 1 of 1, failed: 1
Error executing process > 'CHECK_DESIGN (design.csv)'
Caused by:
Cannot find a matching VM image with publisher=microsoft-azure-batch; offer=centos-container; OS type=linux; verification type=verified
我试着查看 nextflow 的源代码。我发现错误在 AzBatchService.groovy
(下面的行号)中。
我在我的 Azure Batch 帐户实例中做了一些进一步的挖掘。基本上,我想确认从 Azure Batch 帐户收到的支持图像列表是否包含此管道所需的图像。我可以确认服务器确实响应了所需的图像 -
这可能是什么问题?我记得几周前 运行 完全相同的管道,它确实工作了几次。我错过了什么吗?
刚刚又看了一遍 Azure Cloud 文档,认为这可能是相关的:
By default, Nextflow creates CentOS 8-based pool nodes, but this behavior can be customised in the pool configuration. Below the configurations for image reference/SKU combinations to select two popular systems.
- Ubuntu 20.04:
sku = "batch.node.ubuntu 20.04" offer = "ubuntu-server-container" publisher = "microsoft-azure-batch"
- CentOS 8 (default):
sku = "batch.node.centos 8" offer = "centos-container" publisher = "microsoft-azure-batch"
我认为这里的问题是不匹配 nodeAgentSkuId
。 Nextflow 期望 CentOS 8 节点代理 SKU,但您有 CentOS 7 SKU。如果无法以某种方式更改 nodeAgentSkuId
,Nextflow 使用的节点代理 SKU 应该可以通过将其添加到您的 nextflow.config
:
azure.batch.pools.<name>.sku = 'batch.node.centos 7'
其中 <name>
是池标识符:
azure.batch.pools.<name>.sku
Specify the ID of the Compute Node agent SKU which the pool identified with
<name>
supports (default:batch.node.centos 8
, requiresnf-azure@0.11.0
).
https://www.nextflow.io/docs/edge/azure.html#advanced-settings