Bump version up to 1.1.1.

Codecov Report

Merging #260 (bc0ddf3) into main (8db3319) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main     #260   +/-   ##
=======================================
  Coverage   97.67%   97.67%
=======================================
  Files          34       34
  Lines        2275     2275
  Branches      230      230
=======================================
  Hits         2222     2222
  Misses         52       52
  Partials        1        1

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Unable to resolve module ./globalState

I am using numbro inside my react native app project. Unfortunately I got this error.
Error: Unable to resolve module `./globalState` from `${project_directory}\node_modules\numbro\dist\numbro.js`: The module `./globalState` could not be found from `${project_directory}\node_modules\numbro\dist\numbro.js`. Indeed, none of these files exist:

  * `${project_directory}\node_modules\numbro\dist\globalState(.native||.android.js|.native.js|.js|.android.json|.native.json|.json)`
  * `${project_directory}\node_modules\numbro\dist\globalState\index(.native||.android.js|.native.js|.js|.android.json|.native.json|.json)`

It seems that globalState folder is not exist inside dist folder.

is it ok now?

Yes, Mr. @BenjaminVanRyseghem . You can close this issue.


Keypass option for custom keystore

Hi,
I was wondering how a custom keystore can be used that has both a keystore pass and a key pass?
the only options available to pass to Selendroid (regarding a custom keystore) are:
-keystore
-keystoreAlias
-keystorePassword
but to access the key in my keystore, I need to be able to provide a key password.
To compare with Appium, they have options to specify:
-keystore-path => matches with selendroid keystore
-keystore-password => matches with selendroid keystorePassword
-key-alias => matches with selendroid keystoreAlias
-key-password => not supported in selendroid?
Any idea how to make it work with this kind of custom keystore? Should I sign the Selendroid apk myself and use that one somehow? Or should I set a specific default key password to make it work?
Thanks!

Looking further, I found a similar ticket about this: #64
The ticket links to the appium support for this (added with this pull request: appium/appium/pull/807)  but it was closed without any comment of a fix and without a pull request being linked. I think it's not implemented so far?

Hi Pver,
Yes, released version of selendroid doesn't support keypass. I had added support in the current development branch(0.18.0). But not created a pull request yet. If you want I can share the standalone server jar build on my development machine.
Thanks,
Kamesh

Hi @sri096,
I managed to work around it for now by signing the selendroid apk with my certificate and preinstall that before the tests. But great to hear it will be in 0.18.0, thanks for the info!


add useNavigate - single file version

Second version of useNavigate PR, single file, but imports vike/abort and vike/client/router both on the client and server
Alternative implemenation: https://github.com/vikejs/vike-react/pull/123.

but imports vike/abort and vike/client/router both on the client and server

That isn't an issue: navigate() can be imported on the server-side (it throws an error if called on the server-side).

Let's re-open once we work on this again.


Json

:books: Documentation preview :books:: https://mrmoe--146.org.readthedocs.build/en/146/

Codecov Report

Merging #146 (f751ddb) into master (e33f22c) will increase coverage by 0.25%.
The diff coverage is 98.67%.

:exclamation: Current head f751ddb differs from pull request most recent head 6b0c4f1. Consider uploading reports for the commit 6b0c4f1 to get more accurate results

@@            Coverage Diff             @@
##           master     #146      +/-   ##
==========================================
+ Coverage   98.04%   98.29%   +0.25%
==========================================
  Files          35       38       +3
  Lines        1684     1881     +197
==========================================
+ Hits         1651     1849     +198
+ Misses         33       32       -1


After NU5 testnet activation, set the minimum testnet network protocol version to NU5

Motivation
There are only a small number of Zebra instances running right now.
So instead of automatically closing connections to outdated peers, we can just set the testnet minimum protocol version to NU5 after NU5 testnet activation. (But keep the mainnet minimum protocol version at Canopy.)
Then we can upgrade and restart all the running Zebra instances, and they will reject outdated peers from genesis onwards.
Specifications
Original specification: ZIP 201: Network Peer Management for Overwinter
Since this is a network protocol specification, Zebra is free to adopt any compatible design.
Designs
Draft Zebra behaviour: ZIP 252: Deployment of the NU5 Network Upgrade - Support in Zebra
Related Work
This ticket is a smaller temporary substitute for #2262 and #2451.
If we make a similar minimum version change on mainnet, we don't need to implement #2451 at all.
But we still need to implement #2262 for the next network upgrade.

Moving this to sprint 20, because NU5 testnet will activate during that sprint.


Circular import error when using data/packing.py

Hello,
Getting the following circular import error when trying to run the data/packing.py script
using the command below:
python llmfoundry/data/packing.py --yaml-path /home/justin/code/ai/llm-foundry/scripts/train/yamls/finetune/mpt-7b_dolly_sft.yaml
probably worth looking at llm-foundry/llmfoundry/data/__init__.py as this might be the cause of the error
Error:
Traceback (most recent call last):
  File "/home/justin/home/ai/llm-foundry/llmfoundry/data/packing.py", line 264, in <module>
    from llmfoundry import (build_finetuning_dataloader,
  File "/home/justin/home/ai/llm-foundry/llmfoundry/__init__.py", line 8, in <module>
    from llmfoundry.data import (ConcatTokensDataset,
  File "/home/justin/home/ai/llm-foundry/llmfoundry/data/__init__.py", line 7, in <module>
    from llmfoundry.data.finetuning import (Seq2SeqFinetuningCollator,
  File "/home/justin/home/ai/llm-foundry/llmfoundry/data/finetuning/__init__.py", line 5, in <module>
    from llmfoundry.data.finetuning.dataloader import build_finetuning_dataloader
  File "/home/justin/home/ai/llm-foundry/llmfoundry/data/finetuning/dataloader.py", line 14, in <module>
    from llmfoundry.data.finetuning.tasks import dataset_constructor
  File "/home/justin/home/ai/llm-foundry/llmfoundry/data/finetuning/tasks.py", line 38, in <module>
    import datasets
  File "/home/justin/home/ai/llm-foundry/llmfoundry/data/datasets.py", line 15, in <module>
    class NoConcatDataset(IterableDataset):
  File "/home/justin/home/ai/llm-foundry/llmfoundry/data/datasets.py", line 22, in NoConcatDataset
    hf_datasets.Dataset]):
AttributeError: partially initialized module 'datasets' has no attribute 'Dataset' (most likely due to a circular import)

Probably similar error to the following issue: https://github.com/mosaicml/llm-foundry/issues/127

Hello, we pushed a fix in #175 . Closing for now, please re-open if you run into the same issue again!


Prepare Azure Monitor Query for release

API change check
API changes are not detected in this pull request.


Check all updated dependencies

Description
Check if some updates will cause software crashes
Reproduction steps
.

Screenshots
.

ToDo:

[ ] Update axios calls
[ ] test mocha tests
[ ] test iobroker testing

Done


SearchBox Widget: Template options are janky/broken

Do you want to request a feature or report a bug?
bug
What is the version you are using? Always use the latest one before opening a bug issue.
2.2.1 (latest as of post)
All I want to do is override the default magnifier and reset templates (use a different SVG).
There seem to be a number of oddities. First off, the options seems structured differently than most other core widgets. Instead of having a root level templates, and cssClasses props, it instead has root props of magnifier and reset. Nothing inherently broken there, just seems inconsistent (at least with the widgets I'm familiar with).
Second, the cssClasses prop doesn't really seem to work.
Attempt 1:
Try and render a custom template for the magnifier
searchBox(
  container,
  magnifier: {
    template: myCustomSearchSvg,
  },
);

It rendered my svg! However, within an empty span…I was expecting it to still be wrapped by an element with an .ais-search-box--magnifier since, I didn't override cssClasses.
Oh well, Attempt 2:
Try and manually add the class?
searchBox(
  container,
    magnifier: {
      template: myCustomSearchSvg,
      cssClasses: [{root: 'ais-search-box--magnifier'}],
    },
);

Bubkis. Same result as Attempt 1.
Attempt 3:
Try and render a custom template for the reset button
searchBox(
  container,
  reset: {
    template: 'x',
  },
);

Error!

Uncaught TypeError: Cannot read property 'style' of null
at search-box.js:124
at Object.init (connectSearchBox.js:105)
at InstantSearch.js:213
at arrayEach (_arrayEach.js:15)
at forEach (forEach.js:38)
at InstantSearch._init (InstantSearch.js:211)
at InstantSearch.start (InstantSearch.js:168)

Then I post this and gave up. :)

Thanks for this bug report @timkelty 👍

I've been able to reproduce what you describe. We'll be able to fix the bug that prevent you from usage a custom reset button and add some css classes. However we won't be able to change the structure nor make span divs, even though that's an error on our hand when adding the new searchbox in v2.

Thanks @bobylito, will you queue up those breaking changes for v3 then?

I'm wondering how much of these changes are really important, here. These are the changes I'm thinking about:

make <span> into  <div>. I'm not  convinced it makes a huge difference.
use the root css class for configuring the containers (<span> or later maybe <div>). That one disturbs me, I would see it go through
use the main templates attribute for everything template, and not have them nested in the suboption. That one is in my opinion better kept the way it is right now, this way you can't setup a new magnifier without activating the option first.

WDYT @timkelty ? Happy to have your opinions too @vvo :)

make <span> into <div>
Yeah, this doesn't really matter much at all.
use the root css class for configuring the containers
Would this make my above Attempt 1 and Attempt 2 both work?

The most troubling bug was my "Attempt 3", where it just threw an error when to change the reset template. Do any of your changes address this?

The most troubling bug was my "Attempt 3", where it just threw an error when to change the reset template. Do any of your changes address this?

Indeed. There is an open PR for that https://github.com/algolia/instantsearch.js/pull/2585>

use the root css class for configuring the containers

Would this make my above Attempt 1 and Attempt 2 both work?

Yes. It would have removed the friction. The root class is used inside a template, which gets removed when using a custom template.


HUBOT not connecting

Using the latest Rocket.chat 0.32
Using the latest Docker image to connect
[Tue May 31 2016 08:15:37 GMT+0000 (UTC)] INFO Successfully Logged In
[Tue May 31 2016 08:15:37 GMT+0000 (UTC)] INFO Looking up Room ID for: GENERAL
[Tue May 31 2016 08:15:37 GMT+0000 (UTC)] ERROR Unable to get room id: {"error":"error-not-allowed","reason":"Not allowed","details":{"method":"getRoomIdByNameOrId"},"message":"Not allowed [error-not-allowed]","errorType":"Meteor.Error"} Reason: Not allowed

make sure you have created your "bot user" on the chat server, and logged in at least once with that user - and have joined GENERAL.

Check your docker-compose file against the example i added to the docs:
https://github.com/RocketChat/hubot-rocketchat/pull/138/commits/503db8b6592ad7bb0b697f8e0ef276bf5895c187
Got the same error, after adjusting the compose file like in the example, all was working again.

@TheReal1604 so is this hubot section in the same docker-compose file as rocketchat?

@Sing-Li Hi. I have created bot user on the chat server and have loged in but there is no room as general. I thought thats way my bot cannot connect to room general. Any idea ?
When i login with new user general room is there but with bot it doesn't

Sounds like the bot user just didn't have the bot role or the correct permission on the role.
So make sure the user you are logging in via hubot has the bot role.  Then, on the bot role make sure you add the permission view-c-room
Going to go ahead and close this issue out.  Your issue is related to not being able to join the room.  If that doesn't work please open a new issue regarding that.

FYI I got this error when I connected the bot and set a non-existent room in the ROCKETCHAT_ROOM environment variable. All I had to do was create the room and then try again and it worked fine.

Don't know why but calling robot.messageRoom(user.id, 'text') (i.e. send a direct message to a user) doesn't work anymore for me in the latest version in combination with Hubot3. It throws always the error
ERROR [getRoomIdByNameOrId] Error: { isClientSafe: true,
  error: 'error-not-allowed',
  reason: 'Not allowed',
  details: { method: 'getRoomIdByNameOrId' },
  message: 'Not allowed [error-not-allowed]',
  errorType: 'Meteor.Error' }

The bot has the view-c-room permission but as I'm sending the message to a direct channel I'm guessing that this is not the problem.
Luckily I was able to work around this issue by using robot.adapter.sendDirect({user}, 'text') but it doesn't feel right...

Doesn't work for me either on version 0.68.3. Only in public rooms. In private rooms bot doesn't respond and if i set the primary room as private room, it won't even connect with the error stated here.


Discuss how to improve Spark-on-K8s developer workflow

@foxish @varunkatta
We had a discussion on how to improve our workflow. In particular, how we can shorten the 1. maven/sbt build time and 2. docker image build/push time.
I was chatting a bit more on this with @varunkatta. He suggested one could only build k8s module jars and update a distribution with the new jars. @varunkatta Can you comment on how you did this?
It occurred to me that we could extend this idea to docker image building. We could have a base image that has spark core jars, but not k8s module jars. Then the driver and executor images could extend from the base image by adding k8s module jars. Most of the time when we modified our code, we'll only build the child docker images. Hopefully, this will shorten the build/push time.
What do you think?

This is what I did at a high-level. Built kubernetes spark core, and updated the jar which is present in prebuilt tar zipped distribution with the new updated jar freshly built. Steps outline below.
# assumes you are in top level project dir.
./build/mvn -pl resource-managers/kubernetes/core -Pkubernetes -am package -DskipTests;
# assumes you made a distribution named spark-2.1.0-k8s-0.1.0-SNAPSHOT-bin-k8s-20170301.tgz
tar -zxf spark-2.1.0-k8s-0.1.0-SNAPSHOT-bin-k8s-20170301.tgz;
scp resource-managers/kubernetes/core/target/spark-kubernetes_2.11-2.1.0-k8s-0.1.0-SNAPSHOT.jar spark-2.1.0-k8s-0.1.0-SNAPSHOT-bin-k8s-20170301/jars
tar -zcf spark-2.1.0-k8s-0.1.0-SNAPSHOT-bin-k8s-20170301.tgz spark-2.1.0-k8s-0.1.0-SNAPSHOT-bin-k8s-20170301;

I like the idea of having a base docker with all the required spark jars except the spark-kubernetes jar, and incrementally building the new docker image with the freshly baked spark-kubernetes jar.  Curious to see how many seconds it will shave off of current docker image building time.

@kimoonkim or @varunkatta - can either of you ship a PR to use base docker images? Keep in mind to also update SparkDockerImageBuilder in the integration test package also.
One question though is what tag of the base image the child images should depend on. The child dockerfiles reference the parent image by image-name:image-tag, e.g. spark-base:latest or spark-base:2.1. I'm not sure what the right version for the children to depend on is here. Whatever that version is, the SparkDockerImageBuilder in the integration test project needs to tag the base image accordingly.

I will send a send a PR for this.  I am thinking we should use spark-base:latest over using the version number in the tag.

There is PR in the Kubernetes ansible project for this - https://github.com/apache-spark-on-k8s/ansible/pull/4


Make Date type not break.

Currently, the use of Date as a type in a Record breaks, because there is a reference to Typed.Date, which is never actually defined.
This pull request defines it.

👍

I am happy to merge this since you have okayed it, but I need write access.

Added

Merged.


Validation - Skype Relative Links 4

Fixing about 43 docsAbsoluteLinks.
Also removing "?view=ucma-api" from the /dotnet/ links.

Docs Build status updates of commit 3a0e2bb:
:warning: Validation status: warnings

File
Status
Preview URL
Details

Skype/Trusted-Application-API/docs/RegistrationInAzureActiveDirectory.md
:warning:Warning

Details

Skype/Trusted-Application-API/docs/SfBRegistration.md
:warning:Warning

Details

Skype/Trusted-Application-API/samples/AnonMeetingJoinSamples/README.md
:warning:Warning

Details

Skype/Trusted-Application-API/samples/QuickStartSamples/README.md
:warning:Warning

Details

Skype/index.md
:warning:Warning

Details

Skype/UCMA/client-platforms.md
:bulb:Suggestion

Details

Skype/UCMA/communications-conversations-calls-conferences-and-back-to-back-user-agents.md
:bulb:Suggestion

Details

Skype/UCMA/conferencemanagement-quickstart.md
:bulb:Suggestion

Details

Skype/UCMA/connecting-to-audio-resources-in-ucma-5-0.md
:bulb:Suggestion

Details

Skype/UCMA/connection-manager.md
:bulb:Suggestion

Details

Skype/UCMA/contactgroupservices.md
:bulb:Suggestion

Details

Skype/UCMA/contacts-and-groups-management.md
:bulb:Suggestion

Details

Skype/UCMA/contacts-and-groups.md
:bulb:Suggestion

Details

Skype/Trusted-Application-API/docs/RegistrationInAzureActiveDirectory.md

Line 1, Column 1: [Warning: title-missing - See documentation] Missing required attribute: 'title'. Add a title string to show in search engine results.
Line 1, Column 1: [Warning: duplicate-h1s - See documentation] H1 'Registering your application in Azure AD' is duplicated with other articles: 'Trusted-Application-API/docs/RegistrationInAzureActiveDirectory.md, UCWA/RegisteringYourApplicationInAzureAD.md(2,1)'. First level headings must be unique within a docset.
Line 1, Column 1: [Warning: duplicate-titles - See documentation] Title 'Registering your application in Azure AD' is duplicated in: 'Trusted-Application-API/docs/RegistrationInAzureActiveDirectory.md, UCWA/RegisteringYourApplicationInAzureAD.md(2,1)'. Titles must be unique within a docset.
Line 14, Column 2: [Warning: duplicate-alt-text - See documentation] Alt text 'alt text' is duplicated. Within an article, alt text must be unique.
Line 18, Column 2: [Warning: duplicate-alt-text - See documentation] Alt text 'alt text' is duplicated. Within an article, alt text must be unique.
Line 22, Column 2: [Warning: duplicate-alt-text - See documentation] Alt text 'alt text' is duplicated. Within an article, alt text must be unique.
Line 28, Column 2: [Warning: duplicate-alt-text - See documentation] Alt text 'alt text' is duplicated. Within an article, alt text must be unique.
Line 32, Column 2: [Warning: duplicate-alt-text - See documentation] Alt text 'alt text' is duplicated. Within an article, alt text must be unique.
Line 36, Column 2: [Warning: duplicate-alt-text - See documentation] Alt text 'alt text' is duplicated. Within an article, alt text must be unique.
Line 42, Column 2: [Warning: duplicate-alt-text - See documentation] Alt text 'alt text' is duplicated. Within an article, alt text must be unique.
Line 1, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.

Skype/Trusted-Application-API/docs/SfBRegistration.md

Line 1, Column 1: [Warning: title-missing - See documentation] Missing required attribute: 'title'. Add a title string to show in search engine results.
Line 1, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.

Skype/Trusted-Application-API/samples/AnonMeetingJoinSamples/README.md

Line 1, Column 1: [Warning: title-missing - See documentation] Missing required attribute: 'title'. Add a title string to show in search engine results.
Line 1, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.

Skype/Trusted-Application-API/samples/QuickStartSamples/README.md

Line 100, Column 1: [Warning: code-block-indented - See documentation] Indented code blocks aren't allowed. Use a Markdown code block surrounded by triple backticks (```).

Skype/index.md

Line 1, Column 1: [Warning: title-missing - See documentation] Missing required attribute: 'title'. Add a title string to show in search engine results.
Line 1, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.

Skype/UCMA/client-platforms.md

Line 2, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.

Skype/UCMA/communications-conversations-calls-conferences-and-back-to-back-user-agents.md

Line 2, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.

Skype/UCMA/conferencemanagement-quickstart.md

Line 2, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.

Skype/UCMA/connecting-to-audio-resources-in-ucma-5-0.md

Line 2, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.
Line 15, Column 95: [Suggestion: preserve-view-not-set - See documentation] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: /dotnet/api/microsoft.rtc.collaboration.audiovideo.voicexml.browser?view=ucma-voice. Otherwise, remove the view parameter.

Skype/UCMA/connection-manager.md

Line 2, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.
Line 73, Column 321: [Suggestion: preserve-view-not-set - See documentation] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: /dotnet/api/system.net.ipendpoint?view=netframework-4.7.2. Otherwise, remove the view parameter.
Line 73, Column 462: [Suggestion: preserve-view-not-set - See documentation] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: /dotnet/api/system.net.ipendpoint.port?view=netframework-4.7.2. Otherwise, remove the view parameter.
Line 73, Column 593: [Suggestion: preserve-view-not-set - See documentation] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: /dotnet/api/system.net.ipendpoint.address?view=netframework-4.7.2. Otherwise, remove the view parameter.

Skype/UCMA/contactgroupservices.md

Line 2, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.

Skype/UCMA/contacts-and-groups-management.md

Line 2, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.

Skype/UCMA/contacts-and-groups.md

Line 2, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.

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@ShawnVW1 hi Shawn, is this PR still happening or is it abandoned?

Actually, I'm not sure. While the infamous skype-docs was being sorted out, I had to switch to another project.
Meera, what should I do with this now? I'm not sure if I submitted it for peer review yet.

Shawn

From: Linda Lu Cannon @.>
Sent: Monday, April 18, 2022 1:14 PM
To: OfficeDev/skype-docs @.>
Cc: Shawn Wilson (AQUENT LLC) @.>; Mention @.>
Subject: Re: [OfficeDev/skype-docs] Validation - Skype Relative Links 4 (PR #705)
@ShawnVW1https://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FShawnVW1&data=05|01|v-shawwilson%40microsoft.com|b1a612bdb08f4d8c7d7308da2177fe46|72f988bf86f141af91ab2d7cd011db47|1|0|637859096505719715|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=ef6vkMDxn5h1DFUyxvwmhpsf%2Fch1Ejhw21G26Sc%2BEhk%3D&reserved=0 hi Shawn, is this PR still happening or is it abandoned?

Reply to this email directly, view it on GitHubhttps://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FOfficeDev%2Fskype-docs%2Fpull%2F705%23issuecomment-1101724187&data=05|01|v-shawwilson%40microsoft.com|b1a612bdb08f4d8c7d7308da2177fe46|72f988bf86f141af91ab2d7cd011db47|1|0|637859096505719715|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=WTkwZgr9Uulumi92%2F6yOaZbASZ0T41jld6fe323Kzgs%3D&reserved=0, or unsubscribehttps://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAYPBGZJIUWA4H74SU4KQS6DVFW7A7ANCNFSM5TEWZ6WA&data=05|01|v-shawwilson%40microsoft.com|b1a612bdb08f4d8c7d7308da2177fe46|72f988bf86f141af91ab2d7cd011db47|1|0|637859096505719715|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=BW%2B5a6MWBMkF%2BxcPF32e9H7eiJTucAiqVQIVEIcfHcE%3D&reserved=0.
You are receiving this because you were mentioned.Message ID: @.***>

@lindalu-MSFT
This PR is ready for a final reviewer.
The Content & Learning team is fixing build validation errors on docs.microsoft.com for the rest of H2. This will eliminate potential accessibility, security, and usability issues. This PR includes only build validation fixes and does not change other content. Please review within five business days and merge or comment in the PR with any changes you’d like to see. Thank you!

Docs Build status updates of commit 46b0ffc:
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Skype/Trusted-Application-API/docs/SfBRegistration.md
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Skype/UCMA/client-platforms.md
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Skype/UCMA/communications-conversations-calls-conferences-and-back-to-back-user-agents.md
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Skype/UCMA/conferencemanagement-quickstart.md
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Skype/UCMA/connecting-to-audio-resources-in-ucma-5-0.md
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Skype/UCMA/connection-manager.md
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Skype/UCMA/contactgroupservices.md
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Skype/UCMA/contacts-and-groups-management.md
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Skype/UCMA/contacts-and-groups.md
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Skype/Trusted-Application-API/docs/RegistrationInAzureActiveDirectory.md
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Skype/Trusted-Application-API/samples/AnonMeetingJoinSamples/README.md
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Skype/index.md
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Skype/Trusted-Application-API/docs/SfBRegistration.md

Line 2, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.

Skype/UCMA/client-platforms.md

Line 2, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.

Skype/UCMA/communications-conversations-calls-conferences-and-back-to-back-user-agents.md

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Skype/UCMA/conferencemanagement-quickstart.md

Line 2, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.

Skype/UCMA/connecting-to-audio-resources-in-ucma-5-0.md

Line 2, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.
Line 15, Column 95: [Suggestion: preserve-view-not-set - See documentation] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: /dotnet/api/microsoft.rtc.collaboration.audiovideo.voicexml.browser?view=ucma-voice. Otherwise, remove the view parameter.

Skype/UCMA/connection-manager.md

Line 2, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.
Line 73, Column 321: [Suggestion: preserve-view-not-set - See documentation] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: /dotnet/api/system.net.ipendpoint?view=netframework-4.7.2. Otherwise, remove the view parameter.
Line 73, Column 462: [Suggestion: preserve-view-not-set - See documentation] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: /dotnet/api/system.net.ipendpoint.port?view=netframework-4.7.2. Otherwise, remove the view parameter.
Line 73, Column 593: [Suggestion: preserve-view-not-set - See documentation] Did you mean to link to a specific version? It's usually better not to specify a version, so the link always goes to the canonical version. If you really need to link to a specific version, add &preserve-view=true to the URL: /dotnet/api/system.net.ipendpoint.address?view=netframework-4.7.2. Otherwise, remove the view parameter.

Skype/UCMA/contactgroupservices.md

Line 2, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.

Skype/UCMA/contacts-and-groups-management.md

Line 2, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.

Skype/UCMA/contacts-and-groups.md

Line 2, Column 1: [Suggestion: description-missing - See documentation] Missing required attribute: 'description'.

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MB-13885 update SQL Query to fix flaky EDI tests running on local machines

Jira ticket for this change
Summary
This PR updates a sql query call to return the paymentServiceItems in the  order in which each were created. This should help resolve the flaky tests happening on local machines as in certain instances before, the paymentServiceItems were being returned not in the order we expected for the tests in this file
Testing the changes

💻
Running Tests
declare -i cc=0; while go test -count 1 -v ./pkg/services/invoice/...; do
cc+=1; echo $cc
done

Verification Steps for Author
These are to be checked by the author.

[ ] Tested in the Experimental environment (for changes to containers, app startup, or connection to data stores)
[ ] Request review from a member of a different team.
[ ] Have the Jira acceptance criteria been met for this change?

Messages

:book:
:link: MB-13885

  Generated by :no_entry_sign: dangerJS against fd15b202e166b3523f0302c2268d29eb8fd9f250


Bot does not respond

There are times when the bot does not respond or reply. This happens in both private message and group chat. When the bot does reply, it happens a day later. Any insight on why this is happening?

Hey @asdfghjaz ,
I'm terribly sorry about that. If the bot is ever not responding, feel free to message me directly on Telegram at https://t.me/Voxter256
Generally speaking, that happens when the bot goes offline for whatever reason (the last one was automatic windows updates I didn't expect). Telegram puts all of the messages in a queue until the bot comes back online, at which point they are all sent out.
I had originally planned to solve this by hosting it on AWS, but that turned out to be too expensive for the relatively low amount of traffic. (The bot sends some messages that aren't a direct response to another. Because of this and the need for a database, a NAT Gateway needs to be setup to allow communication outside of the VPC the database is in. Unfortunately it is priced for every hour it is provisioned and available, which came out to ~ $30 a month.)
I am currently brainstorming some long term solutions, such as a small raspberry pi cluster hosting Kubernetes, but that likely won't be up until next year's Holiday season.


Allow errors.As to work with reconciler.Events

Changes

:gift: reconciler.Events that wrap errors can be used with the apimachinery errors package, which uses errors.As to compare error types.

/kind enhancement
https://github.com/knative/eventing/issues/5146 involves a bug where we are trying to ignore IsNotFound-type errors in our finalizer, but right now Events can never be used with these apimachinery predicates.
Release Note
- reconciler.Events can be cast to their underlying error types

/lgtm


Autoscrolling improvements

Fixes #23
The auto-scroller now bases its calculations based on the position of the pointer rather than the edges of the draggable element's rect. This change is aligned with how the native HTML 5 Drag & Drop auto-scrolling behaves.
The auto-scroller now also looks at scrollable ancestors in reverse order by default, meaning it will first attempt to scroll the window, and narrow its focus down rather than the old behaviour of looking at scrollable ancestors in order of closeness to the draggable element in the DOM tree. This generally leads to an improved user experience, but can be customized by passing a configuration object to the autoScroll prop that includes a custom sortScrollableAncestors function.

@clauderic I want to try this branch out in my project that uses dnd-kit, but not sure how to point to it, instead of the installed npm @dnd-kit/core package.
How does one achieve this? With yarn link? With a lerna command?

You can try using yalc or just straight up building the branch locally and replacing the distributed assets in your project's local node_modules if you just want to quickly test without setting up anything complicated.
This PR is still a bit of a work in progress, the acceleration and thresholds need a bit of polish. Also considering letting consumers pass in their own autoscroller offsets

@andelkocvjetkovic Thank you. You saved my sanity. @clauderic Maybe you could consider editing your first comment above?


Only show "/" in label expressions when needed

From @csmoore on February 1, 2016 17:57
A few of the label expressions have forward slashes "/" that result in a strange label when the field is not present (see image below).
@abouffard says these "/" are optional and we can substitute with a space which will address the issue shown in the screenshot.

Copied from original issue: Esri/military-features-data#192

This issue was moved to ArcGIS/military-symbology-styles#55


upgrade julia aggregate docs

Is there a reason why we are still on 1.8?

Nope, just hasn't been updated.

Looks like some authentication thing?


Permission encoding order mismatch

For RV64 the ADP bits are encoded like this:

However CGetPerms and CAndPerms expect this order:

The table for encoding RV32 permissions uses the same order (reversed):

It would be much better if these were consistent!
Also did this question get resolved?

@Timmmm : Thanks for pointing this out; indeed, it needs to be fixed! Would you like to create an MR for this?
The TODO has not been resolved.

@tariqkurd-repo you mean remove the TODO and leave as-is? If new useful combinations are found what's the plan for RV32? Use the reserved pattern?


Ensemble error when adding vardict

I tried to run a pipeline on germline data using gatk strelka2 and vardict.
Running only with gatk AND strelka2 finished fine.
Adding vardict gave me the following error in many samples:
[E::bcf_write] Broken VCF record, the number of columns at chrY:26641147 does not match the number of samples (0 vs 1)
' returned non-zero exit status 255.
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/RED/TOOLS/bin/bcbio_nextgen.py", line 245, in <module>
    main(**kwargs)
  File "/RED/TOOLS/bin/bcbio_nextgen.py", line 46, in main
    run_main(**kwargs)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 50, in run_main
    fc_dir, run_info_yaml)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 91, in _run_toplevel
    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 154, in variant2pipeline
    samples = genotype.parallel_variantcall_region(samples, run_parallel)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/genotype.py", line 208, in parallel_variantcall_region
    "vrn_file", ["region", "sam_ref", "config"]))
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/split.py", line 35, in grouped_parallel_split_combine
    final_output = parallel_fn(parallel_name, split_args)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
    return run_multicore(fn, items, config, parallel=parallel)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
    for data in joblib.Parallel(parallel["num_jobs"], batch_size=1, backend="multiprocessing")(joblib.delayed(fn)(*x) for x in items):
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 1016, in __call__
    self.retrieve()
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 908, in retrieve
    self._output.extend(job.get(timeout=self.timeout))
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/multiprocessing/pool.py", line 670, in get
    raise self._value
subprocess.CalledProcessError: Command 'set -o pipefail; unset R_HOME && unset R_LIBS && export PATH=/RED/RESOURCES/bcbio/anaconda/bin:"$PATH" && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx3500m -XX:+UseSerialGC -Djava.io.tmpdir=/mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/1781F/work/bcbiotx/tmph4gpqeo4' && vardict-java -G /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa -N 1781F -b /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/1781F/work/align/1781F/1781F-sort.bam -c 1 -S 2 -E 3 -g 4 --nosv --deldupvar -Q 10 -F 0x700 /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/1781F/work/vardict/chrY/1781F-chrY_16481226_56685608-unmerged-regions-regionlimit.bed -f 0.1 | /RED/RESOURCES/bcbio/anaconda/bin/teststrandbias.R | /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl -A -N 1781F -E -f 0.1 | grep -v ^##contig | bcftools annotate -h /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/1781F/work/bcbiotx/tmph4gpqeo4/1781F-chrY_16481226_56685608-contig_header.txt | bcftools filter -i 'QUAL >= 0'  | bcftools filter --soft-filter 'LowFreqBias' --mode '+' -e  'FORMAT/AF[0:0] < 0.02 && FORMAT/VD[0] < 30 && INFO/SBF < 0.1 && INFO/NM >= 2.0' |  awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' |  awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /RED/RESOURCES/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/1781F/work/bcbiotx/tmph4gpqeo4/1781F-chrY_16481226_56685608.vcf.gz
Use of uninitialized value $start in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 138, <> line 32.
Use of uninitialized value $end in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 138, <> line 32.
Use of uninitialized value $ref in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 138, <> line 32.
Use of uninitialized value $alt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 138, <> line 32.
Use of uninitialized value $rrev in addition (+) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 141, <> line 32.
Use of uninitialized value $rfwd in addition (+) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 141, <> line 32.
Use of uninitialized value $oddratio in string eq at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 142, <> line 32.
Use of uninitialized value $oddratio in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 144, <> line 32.
Use of uninitialized value $oddratio in numeric gt (>) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 144, <> line 32.
Use of uninitialized value $dp in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 148, <> line 32.
Use of uninitialized value $hiaf in multiplication (*) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 149, <> line 32.
Use of uninitialized value $hicnt in multiplication (*) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 149, <> line 32.
Use of uninitialized value $hicnt in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 151, <> line 32.
Use of uninitialized value $hiaf in multiplication (*) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 152, <> line 32.
Use of uninitialized value $hicnt in multiplication (*) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 152, <> line 32.
Use of uninitialized value $af in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 154, <> line 32.
Use of uninitialized value $pmean in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 155, <> line 32.
Use of uninitialized value $pstd in numeric eq (==) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 156, <> line 32.
Use of uninitialized value $af in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 156, <> line 32.
Use of uninitialized value $qual in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 157, <> line 32.
Use of uninitialized value $mapq in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 158, <> line 32.
Use of uninitialized value $af in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 158, <> line 32.
Use of uninitialized value $sn in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 159, <> line 32.
Use of uninitialized value $nm in numeric gt (>) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 161, <> line 32.
Use of uninitialized value $msi in numeric gt (>) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 162, <> line 32.
Use of uninitialized value $msi in numeric ge (>=) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 162, <> line 32.
Use of uninitialized value $hiaf in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 165, <> line 32.
Use of uninitialized value $bias in string eq at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 165, <> line 32.
Use of uninitialized value in subtraction (-) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 169, <> line 32.
Use of uninitialized value in subtraction (-) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 169, <> line 32.
Use of uninitialized value $msilen in numeric eq (==) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 169, <> line 32.
Use of uninitialized value $hiaf in numeric le (<=) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 170, <> line 32.
Use of uninitialized value $msi in numeric ge (>=) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 170, <> line 32.
Use of uninitialized value $hiaf in numeric le (<=) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 172, <> line 32.
Use of uninitialized value $msi in numeric ge (>=) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 172, <> line 32.
Use of uninitialized value $bias in substitution (s///) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 184, <> line 32.
Use of uninitialized value $vd in string le at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 185, <> line 32.
Use of uninitialized value $alt in pattern match (m//) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 194, <> line 32.
Use of uninitialized value $ref in string eq at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 211, <> line 32.
Use of uninitialized value $alt in string eq at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 211, <> line 32.
Use of uninitialized value $vd in string ne at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 224, <> line 32.
Use of uninitialized value $vd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 225, <> line 32.
Use of uninitialized value $start in join or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $ref in join or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $dp in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $vd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $af in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $bias in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $rfwd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $rrev in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $vfwd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $vrev in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $pmean in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $pstd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $qual in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $qstd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $sbf in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $oddratio in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $mapq in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $sn in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $hiaf in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $adjaf in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $shift3 in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $msi in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $msilen in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $nm in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $hicnt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $hicov in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $lseq in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $rseq in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $dp in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $vd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $af in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $rfwd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $rrev in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $vfwd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $vrev in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 32.
Use of uninitialized value $chrt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $start in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $end in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $ref in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $alt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $chrt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $start in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $end in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $ref in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $alt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $chrt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $start in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $end in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $ref in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $alt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $chrt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $start in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $end in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $ref in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
Use of uninitialized value $alt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 32.
[W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.)
Encountered error, cannot proceed. Please check the error output above.
[E::bcf_write] Broken VCF record, the number of columns at chrY:26641147 does not match the number of samples (0 vs 1)
' returned non-zero exit status 255.

My config is this:
details:
- algorithm:
    aligner: bwa
    effects: vep
    ensemble:
      numpass: 2
      use_filtered: false
    mark_duplicates: true
    realign: false
    recalibrate: false
    save_diskspace: true
    tools_on:
    - vep_splicesite_annotations
    - noalt_calling
    variantcaller:
    - gatk-haplotype
    - strelka2
    - vardict
  analysis: variant2
  description: 1781F
  files:
  - /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/1781F/input/SRR6701499_1.fastq.gz
  - /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/1781F/input/SRR6701499_2.fastq.gz
  genome_build: hg38
  metadata:
    sex: female
fc_name: 1781F
upload:
  dir: ../final

This error repeated many many times in the log. Any thoughts?

Konstantinos;
Thank you for the detailed report and apologies about the issue. Vardict appears to be having trouble calling on the chrY region in these samples and is producing something that the vcf conversion script does not like, resulting in the downstream error from bcftools. If you want to debug this in detail we'd probably need to have the input BAM file in the chrY region that is failing along with the BED regions file.
Practically for your analysis, vardict is probably not the best choice for germline calling. If you'd like to do ensemble with a third caller, I'd recommend samtools as an alternative that's been better tested on germline calling. Hope that substitution is an option to get your analysis finished and happy to talk dig more on vardict if you want to stick with it. Hope this helps.

@chapmanb I wanted to use a more sophisticated caller than samtools. Replacing vardict with deepvariant produces the same error.
https://drive.google.com/drive/folders/1ZKo6-lmdP_AqdTjVYuA8CywWboci4g47?usp=sharing
This is the project folder!

@chapmanb With deepvariant I get the following error:
[2019-10-22T12:13Z] ImportError: No module named _multiarray_umath
[2019-10-22T12:13Z] ImportError: numpy.core._multiarray_umath failed to import
[2019-10-22T12:13Z] ImportError: numpy.core.umath failed to import
[2019-10-22T12:13Z] 2019-10-22 15:13:02.181987: F tensorflow/python/lib/core/bfloat16.cc:675] Check failed: PyBfloat16_Type.tp_base != nullptr
[2019-10-22T12:13Z] parallel: This job failed:
[2019-10-22T12:13Z] /RED/RESOURCES/bcbio/anaconda/envs/dv/bin/python /RED/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.8.0-0/binaries/DeepVariant/0.8.0/DeepVariant-0.8.0/make_examples.zip --mode calling --ref /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/align/178F/178F-sort.bam --regions /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chrY/178F-chrY_16096822_56674002-regions.bed --examples<EMAIL_ADDRESS>--task 0
[2019-10-22T12:13Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/align/178F/178F-sort.bam --regions /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chrY/178F-chrY_16096822_56674002-regions.bed --logdir /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chrY/178F-chrY_16096822_56674002-work/log --examples /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/bcbiotx/tmpiqr9hez3 --sample 178F
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s ImportError: No module named _multiarray_umath
ImportError: No module named _multiarray_umath
ImportError: numpy.core._multiarray_umath failed to import
ImportError: numpy.core.umath failed to import
2019-10-22 15:13:02.181987: F tensorflow/python/lib/core/bfloat16.cc:675] Check failed: PyBfloat16_Type.tp_base != nullptr
parallel: This job failed:
/RED/RESOURCES/bcbio/anaconda/envs/dv/bin/python /RED/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.8.0-0/binaries/DeepVariant/0.8.0/DeepVariant-0.8.0/make_examples.zip --mode calling --ref /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/align/178F/178F-sort.bam --regions /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chrY/178F-chrY_16096822_56674002-regions.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 250.
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s ImportError: No module named _multiarray_umath
[2019-10-22T12:13Z] ImportError: No module named _multiarray_umath
[2019-10-22T12:13Z] ImportError: numpy.core._multiarray_umath failed to import
[2019-10-22T12:13Z] ImportError: numpy.core.umath failed to import
[2019-10-22T12:13Z] 2019-10-22 15:13:02.181833: F tensorflow/python/lib/core/bfloat16.cc:675] Check failed: PyBfloat16_Type.tp_base != nullptr
[2019-10-22T12:13Z] parallel: This job failed:
[2019-10-22T12:13Z] /RED/RESOURCES/bcbio/anaconda/envs/dv/bin/python /RED/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.8.0-0/binaries/DeepVariant/0.8.0/DeepVariant-0.8.0/make_examples.zip --mode calling --ref /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/align/178F/178F-sort.bam --regions /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chr3/178F-chr3_80451540_96543172-regions.bed --examples<EMAIL_ADDRESS>--task 0
[2019-10-22T12:13Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/align/178F/178F-sort.bam --regions /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chr3/178F-chr3_80451540_96543172-regions.bed --logdir /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chr3/178F-chr3_80451540_96543172-work/log --examples /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/bcbiotx/tmpeke97wht --sample 178F
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s ImportError: No module named _multiarray_umath
ImportError: No module named _multiarray_umath
ImportError: numpy.core._multiarray_umath failed to import
ImportError: numpy.core.umath failed to import
2019-10-22 15:13:02.181833: F tensorflow/python/lib/core/bfloat16.cc:675] Check failed: PyBfloat16_Type.tp_base != nullptr
parallel: This job failed:
/RED/RESOURCES/bcbio/anaconda/envs/dv/bin/python /RED/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.8.0-0/binaries/DeepVariant/0.8.0/DeepVariant-0.8.0/make_examples.zip --mode calling --ref /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/align/178F/178F-sort.bam --regions /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chr3/178F-chr3_80451540_96543172-regions.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 250.
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s ImportError: No module named _multiarray_umath
[2019-10-22T12:13Z] ImportError: No module named _multiarray_umath
[2019-10-22T12:13Z] ImportError: numpy.core._multiarray_umath failed to import
[2019-10-22T12:13Z] ImportError: numpy.core.umath failed to import
[2019-10-22T12:13Z] 2019-10-22 15:13:02.181878: F tensorflow/python/lib/core/bfloat16.cc:675] Check failed: PyBfloat16_Type.tp_base != nullptr
[2019-10-22T12:13Z] parallel: This job failed:
[2019-10-22T12:13Z] /RED/RESOURCES/bcbio/anaconda/envs/dv/bin/python /RED/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.8.0-0/binaries/DeepVariant/0.8.0/DeepVariant-0.8.0/make_examples.zip --mode calling --ref /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/align/178F/178F-sort.bam --regions /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chr15/178F-chr15_0_17011839-regions.bed --examples<EMAIL_ADDRESS>--task 0
[2019-10-22T12:13Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/align/178F/178F-sort.bam --regions /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chr15/178F-chr15_0_17011839-regions.bed --logdir /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chr15/178F-chr15_0_17011839-work/log --examples /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/bcbiotx/tmpd4623uew --sample 178F
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s ImportError: No module named _multiarray_umath
ImportError: No module named _multiarray_umath
ImportError: numpy.core._multiarray_umath failed to import
ImportError: numpy.core.umath failed to import
2019-10-22 15:13:02.181878: F tensorflow/python/lib/core/bfloat16.cc:675] Check failed: PyBfloat16_Type.tp_base != nullptr
parallel: This job failed:
/RED/RESOURCES/bcbio/anaconda/envs/dv/bin/python /RED/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.8.0-0/binaries/DeepVariant/0.8.0/DeepVariant-0.8.0/make_examples.zip --mode calling --ref /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/align/178F/178F-sort.bam --regions /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chr15/178F-chr15_0_17011839-regions.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 250.
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s ImportError: No module named _multiarray_umath
[2019-10-22T12:13Z] ImportError: No module named _multiarray_umath
[2019-10-22T12:13Z] ImportError: numpy.core._multiarray_umath failed to import
[2019-10-22T12:13Z] ImportError: numpy.core.umath failed to import
[2019-10-22T12:13Z] 2019-10-22 15:13:02.182070: F tensorflow/python/lib/core/bfloat16.cc:675] Check failed: PyBfloat16_Type.tp_base != nullptr
[2019-10-22T12:13Z] parallel: This job failed:
[2019-10-22T12:13Z] /RED/RESOURCES/bcbio/anaconda/envs/dv/bin/python /RED/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.8.0-0/binaries/DeepVariant/0.8.0/DeepVariant-0.8.0/make_examples.zip --mode calling --ref /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/align/178F/178F-sort.bam --regions /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chr1/178F-chr1_143185672_159277705-regions.bed --examples<EMAIL_ADDRESS>--task 0
[2019-10-22T12:13Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/align/178F/178F-sort.bam --regions /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chr1/178F-chr1_143185672_159277705-regions.bed --logdir /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chr1/178F-chr1_143185672_159277705-work/log --examples /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/bcbiotx/tmp1tnlr40u --sample 178F
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s ImportError: No module named _multiarray_umath
ImportError: No module named _multiarray_umath
ImportError: numpy.core._multiarray_umath failed to import
ImportError: numpy.core.umath failed to import
2019-10-22 15:13:02.182070: F tensorflow/python/lib/core/bfloat16.cc:675] Check failed: PyBfloat16_Type.tp_base != nullptr
parallel: This job failed:
/RED/RESOURCES/bcbio/anaconda/envs/dv/bin/python /RED/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.8.0-0/binaries/DeepVariant/0.8.0/DeepVariant-0.8.0/make_examples.zip --mode calling --ref /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/align/178F/178F-sort.bam --regions /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chr1/178F-chr1_143185672_159277705-regions.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 250.
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/multiprocessing/pool.py", line 119, in worker
    result = (True, func(*args, **kwds))
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 600, in __call__
    return self.func(*args, **kwargs)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 256, in __call__
    for func, args, kwargs in self.items]
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 256, in <listcomp>
    for func, args, kwargs in self.items]
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/utils.py", line 55, in wrapper
    return f(*args, **kwargs)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/multitasks.py", line 315, in variantcall_sample
    return genotype.variantcall_sample(*args)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/genotype.py", line 377, in variantcall_sample
    out_file = caller_fn(align_bams, items, ref_file, assoc_files, region, out_file)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/deepvariant.py", line 24, in run
    region, out_file)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/deepvariant.py", line 32, in _run_germline
    example_dir = _make_examples(bam_file, data, ref_file, region_bed, out_file, work_dir)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/deepvariant.py", line 52, in _make_examples
    do.run(cmd, "DeepVariant make_examples %s" % dd.get_sample_name(data))
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/align/178F/178F-sort.bam --regions /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chrY/178F-chrY_16096822_56674002-regions.bed --logdir /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chrY/178F-chrY_16096822_56674002-work/log --examples /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/bcbiotx/tmpiqr9hez3 --sample 178F
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s ImportError: No module named _multiarray_umath
ImportError: No module named _multiarray_umath
ImportError: numpy.core._multiarray_umath failed to import
ImportError: numpy.core.umath failed to import
2019-10-22 15:13:02.181987: F tensorflow/python/lib/core/bfloat16.cc:675] Check failed: PyBfloat16_Type.tp_base != nullptr
parallel: This job failed:
/RED/RESOURCES/bcbio/anaconda/envs/dv/bin/python /RED/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.8.0-0/binaries/DeepVariant/0.8.0/DeepVariant-0.8.0/make_examples.zip --mode calling --ref /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/align/178F/178F-sort.bam --regions /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chrY/178F-chrY_16096822_56674002-regions.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 250.
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/RED/TOOLS/bin/bcbio_nextgen.py", line 245, in <module>
    main(**kwargs)
  File "/RED/TOOLS/bin/bcbio_nextgen.py", line 46, in main
    run_main(**kwargs)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 50, in run_main
    fc_dir, run_info_yaml)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 91, in _run_toplevel
    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 154, in variant2pipeline
    samples = genotype.parallel_variantcall_region(samples, run_parallel)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/genotype.py", line 208, in parallel_variantcall_region
    "vrn_file", ["region", "sam_ref", "config"]))
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/split.py", line 35, in grouped_parallel_split_combine
    final_output = parallel_fn(parallel_name, split_args)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
    return run_multicore(fn, items, config, parallel=parallel)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
    for data in joblib.Parallel(parallel["num_jobs"], batch_size=1, backend="multiprocessing")(joblib.delayed(fn)(*x) for x in items):
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 1016, in __call__
    self.retrieve()
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 908, in retrieve
    self._output.extend(job.get(timeout=self.timeout))
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/multiprocessing/pool.py", line 670, in get
    raise self._value
subprocess.CalledProcessError: Command 'dv_make_examples.py --cores 1 --ref /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/align/178F/178F-sort.bam --regions /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chrY/178F-chrY_16096822_56674002-regions.bed --logdir /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chrY/178F-chrY_16096822_56674002-work/log --examples /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/bcbiotx/tmpiqr9hez3 --sample 178F
Computers / CPU cores / Max jobs to run
1:local / 20 / 1
Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete
ETA: 0s Left: 1 AVG: 0.00s  local:1/0/100%/0.0s ImportError: No module named _multiarray_umath
ImportError: No module named _multiarray_umath
ImportError: numpy.core._multiarray_umath failed to import
ImportError: numpy.core.umath failed to import
2019-10-22 15:13:02.181987: F tensorflow/python/lib/core/bfloat16.cc:675] Check failed: PyBfloat16_Type.tp_base != nullptr
parallel: This job failed:
/RED/RESOURCES/bcbio/anaconda/envs/dv/bin/python /RED/RESOURCES/bcbio/anaconda/envs/dv/share/deepvariant-0.8.0-0/binaries/DeepVariant/0.8.0/DeepVariant-0.8.0/make_examples.zip --mode calling --ref /RED/RESOURCES/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --reads /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/align/178F/178F-sort.bam --regions /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/178F/work/deepvariant/chrY/178F-chrY_16096822_56674002-regions.bed --examples<EMAIL_ADDRESS>--task 0
' returned non-zero exit status 250.

@chapmanb
There is something strange happening. Strelka2 calls 4x more variants than all other callers (GATK, Octopus, Samtools)! I think you should check this out to see what happens!
gatk.zip
samtools.zip
gatk-strelka2-octopus.zip
strelka2.zip
gatk-strelka-samtools.zip
octopus.zip

Konstantinos;
Thanks for all the details and additonal information. It looks like the general issue here is that you're calling targeted exome data without the corresponding variant_regions BED file of targets. Without narrowing to target regions you can end up calling in low depth off target regions. This appears to be causing the edge cases you see with vardict and deepvariant since it's being asked to call in small low coverage regions. It likely also has an impact on the call differences you'll see between methods.
I'd recommend re-running the analysis with a variant_regions BED corresponding to your target regions. Hopefully this will help resolve these issues and give you more consistent results.

Thanks @chapmanb ! WIll try and report back!

Vardict does not work with the specified bed file:
The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/RED/TOOLS/bin/bcbio_nextgen.py", line 245, in <module>
    main(**kwargs)
  File "/RED/TOOLS/bin/bcbio_nextgen.py", line 46, in main
    run_main(**kwargs)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 50, in run_main
    fc_dir, run_info_yaml)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 91, in _run_toplevel
    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/pipeline/main.py", line 154, in variant2pipeline
    samples = genotype.parallel_variantcall_region(samples, run_parallel)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/variation/genotype.py", line 208, in parallel_variantcall_region
    "vrn_file", ["region", "sam_ref", "config"]))
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/split.py", line 35, in grouped_parallel_split_combine
    final_output = parallel_fn(parallel_name, split_args)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
    return run_multicore(fn, items, config, parallel=parallel)
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
    for data in joblib.Parallel(parallel["num_jobs"], batch_size=1, backend="multiprocessing")(joblib.delayed(fn)(*x) for x in items):
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 1016, in __call__
    self.retrieve()
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 908, in retrieve
    self._output.extend(job.get(timeout=self.timeout))
  File "/RED/RESOURCES/bcbio/anaconda/lib/python3.6/multiprocessing/pool.py", line 670, in get
    raise self._value
subprocess.CalledProcessError: Command 'set -o pipefail; unset R_HOME && unset R_LIBS && export PATH=/RED/RESOURCES/bcbio/anaconda/bin:"$PATH" && unset JAVA_HOME &&export VAR_DICT_OPTS='-Xms750m -Xmx3500m -XX:+UseSerialGC -Djava.io.tmpdir=/mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/381F/work/bcbiotx/tmpp1ylabq5' && vardict-java -G /RED/RESOURCES/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -N 381F -b /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/381F/work/align/381F/381F-sort.bam -c 1 -S 2 -E 3 -g 4 --nosv --deldupvar -Q 10 -F 0x700 /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/381F/work/vardict/Y/381F-Y_15526534_59222281-unmerged-regions-regionlimit.bed -f 0.1 | /RED/RESOURCES/bcbio/anaconda/bin/teststrandbias.R | /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl -A -N 381F -E -f 0.1 | grep -v ^##contig | bcftools annotate -h /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/381F/work/bcbiotx/tmpp1ylabq5/381F-Y_15526534_59222281-contig_header.txt | bcftools filter -i 'QUAL >= 0'  | bcftools filter --soft-filter 'LowFreqBias' --mode '+' -e  'FORMAT/AF[0:0] < 0.02 && FORMAT/VD[0] < 30 && INFO/SBF < 0.1 && INFO/NM >= 2.0' |  awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' |  awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /RED/RESOURCES/bcbio/anaconda/bin/vcfstreamsort | bgzip -c > /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/381F/work/bcbiotx/tmpp1ylabq5/381F-Y_15526534_59222281.vcf.gz
Use of uninitialized value $chrt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 138, <> line 8.
Use of uninitialized value $start in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 138, <> line 8.
Use of uninitialized value $end in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 138, <> line 8.
Use of uninitialized value $ref in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 138, <> line 8.
Use of uninitialized value $alt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 138, <> line 8.
Use of uninitialized value $rrev in addition (+) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 141, <> line 8.
Use of uninitialized value $rfwd in addition (+) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 141, <> line 8.
Use of uninitialized value $oddratio in string eq at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 142, <> line 8.
Use of uninitialized value $oddratio in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 144, <> line 8.
Use of uninitialized value $oddratio in numeric gt (>) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 144, <> line 8.
Use of uninitialized value $dp in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 148, <> line 8.
Use of uninitialized value $hiaf in multiplication (*) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 149, <> line 8.
Use of uninitialized value $hicnt in multiplication (*) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 149, <> line 8.
Use of uninitialized value $hicnt in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 151, <> line 8.
Use of uninitialized value $hiaf in multiplication (*) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 152, <> line 8.
Use of uninitialized value $hicnt in multiplication (*) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 152, <> line 8.
Use of uninitialized value $af in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 154, <> line 8.
Use of uninitialized value $pmean in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 155, <> line 8.
Use of uninitialized value $pstd in numeric eq (==) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 156, <> line 8.
Use of uninitialized value $af in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 156, <> line 8.
Use of uninitialized value $qual in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 157, <> line 8.
Use of uninitialized value $mapq in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 158, <> line 8.
Use of uninitialized value $af in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 158, <> line 8.
Use of uninitialized value $sn in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 159, <> line 8.
Use of uninitialized value $nm in numeric gt (>) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 161, <> line 8.
Use of uninitialized value $msi in numeric gt (>) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 162, <> line 8.
Use of uninitialized value $msi in numeric ge (>=) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 162, <> line 8.
Use of uninitialized value $hiaf in numeric lt (<) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 165, <> line 8.
Use of uninitialized value $bias in string eq at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 165, <> line 8.
Use of uninitialized value in subtraction (-) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 169, <> line 8.
Use of uninitialized value in subtraction (-) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 169, <> line 8.
Use of uninitialized value $msilen in numeric eq (==) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 169, <> line 8.
Use of uninitialized value $hiaf in numeric le (<=) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 170, <> line 8.
Use of uninitialized value $msi in numeric ge (>=) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 170, <> line 8.
Use of uninitialized value $hiaf in numeric le (<=) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 172, <> line 8.
Use of uninitialized value $msi in numeric ge (>=) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 172, <> line 8.
Use of uninitialized value $bias in substitution (s///) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 184, <> line 8.
Use of uninitialized value $vd in string le at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 185, <> line 8.
Use of uninitialized value $alt in pattern match (m//) at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 194, <> line 8.
Use of uninitialized value $ref in string eq at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 211, <> line 8.
Use of uninitialized value $alt in string eq at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 211, <> line 8.
Use of uninitialized value $vd in string ne at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 224, <> line 8.
Use of uninitialized value $vd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 225, <> line 8.
Use of uninitialized value $start in join or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $ref in join or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $dp in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $vd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $af in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $bias in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $rfwd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $rrev in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $vfwd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $vrev in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $pmean in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $pstd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $qual in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $qstd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $sbf in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $oddratio in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $mapq in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $sn in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $hiaf in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $adjaf in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $shift3 in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $msi in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $msilen in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $nm in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $hicnt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $hicov in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $lseq in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $rseq in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $dp in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $vd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $af in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $rfwd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $rrev in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $vfwd in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $vrev in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 231, <> line 8.
Use of uninitialized value $chrt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $start in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $end in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $ref in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $alt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $chrt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $start in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $end in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $ref in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $alt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $chrt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $start in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $end in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $ref in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $alt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $chrt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $start in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $end in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $ref in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
Use of uninitialized value $alt in concatenation (.) or string at /RED/RESOURCES/bcbio/anaconda/bin/var2vcf_valid.pl line 137, <> line 8.
[W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.)
Encountered error, cannot proceed. Please check the error output above.
' returned non-zero exit status 255.

exome_hg19.zip

Konstantinos,
Your BED file has chromosomes named like 1,2,3,4,Y but should be named chr1,chr2,chr3 etc.

It is also hg19 whereas your config above specifies hg38?

Also you need to be careful about the coordinate.... yeah, what Oliver said.

My config is this
details:
- algorithm:
    aligner: bwa
    effects: vep
    ensemble:
      numpass: 2
      use_filtered: false
    mark_duplicates: true
    realign: false
    recalibrate: false
    save_diskspace: true
    tools_on:
    - vep_splicesite_annotations
    - noalt_calling
    variant_regions: /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/381F/exome_hg19.bed
    variantcaller:
    - gatk-haplotype
    - strelka2
    - samtools
    - octopus
  analysis: variant2
  description: 381F
  files:
  - /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/381F/input/SRR6701472_1.fastq.gz
  - /mnt/36642bae-9ec9-4100-88a2-ac173a20ea16/WORKDIR/BRAZILIANS/381F/input/SRR6701472_2.fastq.gz
  genome_build: GRCh37
  metadata:
    sex: female
fc_name: 381F
upload:
  dir: ../final

I think that config file is different than the GATK file you posted, because what you posted has hg38 in the header, do grep hg38 gatk.vcf and you'll see.

Yes, it is another run. I used a bed file from illumina which was on GRCh37 coordinates

Oh, I see. Sorry, we were confused. Those are all right for GRCh37 then, except in the BED file chrM should be MT.

Same. Run it again from the start with the corrected bed
exome_hg19.zip

Even with a specified targeted exome bed file, Strelka2 gives 4-5x more variants than other callers.
strelka2.zip
samtools.zip
octopus.zip
gatk.zip
ensemble.zip

Konstantinos;
Thanks for following up with the additional details and information. You're exactly right that strelka2, and most variant callers, contain soft filtered variants where the VCF has a non-PASS flag in the FILTER field. These are included to help with identifying variants in cases where filters are too strict, but generally you should count and analyze on the PASS variants.
Looking at the MultiQC report for your sample, the issue looks to be the low coverage of this dataset. Even with the variant BED set, you only have under 50% of the reads mapping to the targets and an overall low coverage of 8x across your sample. vardict and deeepvariant aren't likely to work well on low coverage capture input data, and you're continuing to see these edge cases where you have a small region with limited coverage.
For digging more into this dataset, I'd suggest focusing on determining why you have such low on-target and overall coverage in the sample. This is hard for us to diagnose, but following up with the lab team that created the sample might help identify what is going on so you can improve coverage and make use of additional callers.
Thanks again for all the debugging and hope this helps.

@chapmanb ;
Thank you for your valuable info!


[VC] pluggable syncer

syncer: add BaseResourceSyncer for inheritance
syncer: introduce plugin mechanism

Signed-off-by: zhuangqh<EMAIL_ADDRESS>

/lgtm
/approve