From d95e7265c00a9bf3ca85754e6ff2ea236ec1ba6b Mon Sep 17 00:00:00 2001 From: Harmon Date: Wed, 29 Jan 2025 19:35:53 +0000 Subject: [PATCH 1/4] Added instructions on what to do if you run out of container API requests --- docs/troubleshooting.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/docs/troubleshooting.md b/docs/troubleshooting.md index ce7d7b6e..2c704c03 100644 --- a/docs/troubleshooting.md +++ b/docs/troubleshooting.md @@ -26,3 +26,19 @@ Jobs may sometimes fail due to insufficient memory or CPU availability, especial - **Increase resource allocations in `configs/resources.config`.** This will alter the resources available to all processes with a given tag (e.g. "small"). - **Increase resource allocation to a specific process.** You can do this by editing the process in the relevant Nextflow file, most likely found at `modules/local/MODULE_NAME/main.nf`. Note that in some cases it may not be possible to allocate enough resources to meet the needs of a given process, especially on a resource-constrained machine. In this case, you will need to use a smaller reference file (e.g. a smaller Kraken reference DB) or obtain a larger machine. + +## API container errors + +Jobs may sometimes fail due to using up [too many API requests to get the containers](https://docs.seqera.io/wave/api). This will look like the following: + +``` +Task failed to start - CannotPullImageManifestError: Error response from daemon: toomanyrequests: Request exceeded pull rate limit for IP XX.XXX.XX.XX +``` + +To fix this, you can: +1. Create a seqera account [here](http://cloud.seqera.io/) for free. +2. Click on the user icon, then click the 'User tokens' section. +3. Now click 'Add Token' to create a token for your account. Name it whatever you want (e.g. "my-nextflow-token"). Copy the token, and store it somewhere. +4. Navigate yourself to this repo, open the profiles config file (`configs/profiles.config`), and add in the following line `tower.accessToken=`, where `` is the token you generated in the last step. +This will increase your API limit by 4x. If you still keep running into this same issue, you may consider contacting Seqera for more options. + From 5f2afd2a6ea80ff45536273a88b24fa5a19e8017 Mon Sep 17 00:00:00 2001 From: Harmon Date: Wed, 29 Jan 2025 19:36:41 +0000 Subject: [PATCH 2/4] Added another fix --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d2217a35..8cb7a097 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,6 @@ +# v2.7.0.1 +- Added instructions for what to do should you run out of API requests for containers + # v2.7.0.0 - Implemented masking of viral genome reference in index workflow with MASK_GENOME_FASTA to remove adapter, low-entropy and repeat sequences. - Removed TRIMMOMATIC and BBMAP from EXTRACT_VIRAL_READS. From 28c004e7957667163d55dd00f54543194b051b55 Mon Sep 17 00:00:00 2001 From: Harmon Bhasin Date: Thu, 30 Jan 2025 11:44:17 -0500 Subject: [PATCH 3/4] Update troubleshooting.md fix incorrect backtick --- docs/troubleshooting.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/troubleshooting.md b/docs/troubleshooting.md index 2c704c03..26b745bb 100644 --- a/docs/troubleshooting.md +++ b/docs/troubleshooting.md @@ -39,6 +39,6 @@ To fix this, you can: 1. Create a seqera account [here](http://cloud.seqera.io/) for free. 2. Click on the user icon, then click the 'User tokens' section. 3. Now click 'Add Token' to create a token for your account. Name it whatever you want (e.g. "my-nextflow-token"). Copy the token, and store it somewhere. -4. Navigate yourself to this repo, open the profiles config file (`configs/profiles.config`), and add in the following line `tower.accessToken=`, where `` is the token you generated in the last step. +4. Navigate yourself to this repo, open the profiles config file (`configs/profiles.config`), and add in the following line `tower.accessToken=`, where `` is the token you generated in the last step. This will increase your API limit by 4x. If you still keep running into this same issue, you may consider contacting Seqera for more options. From 4c1f9ac84586f71c3bc7bb3cb1d203fbb586a761 Mon Sep 17 00:00:00 2001 From: Harmon Bhasin Date: Thu, 30 Jan 2025 14:47:02 -0500 Subject: [PATCH 4/4] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8cb7a097..46fcdaf5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,4 @@ -# v2.7.0.1 +# v2.7.0.1 (in-progress) - Added instructions for what to do should you run out of API requests for containers # v2.7.0.0