WeibullAFTFitter does not ignore the index of the DataFrame and errors (NaNs were detected in the dataset.)

Show by example:
from lifelines import WeibullAFTFitter
import pandas as pd

data = pd.DataFrame({'duration': np.arange(1, 11), 'event': np.ones(10), 'x0': np.arange(1, 11)})

regr = WeibullAFTFitter()
regr.fit(data, duration_col='duration', event_col='event')

That works fine. But if I take a row subset of the data so the DataFrame index isn't arange:
sub_data = data[[True, False]*5]
regr = WeibullAFTFitter()
regr.fit(sub_data, duration_col='duration', event_col='event')

It produces the following error even though there is no inf or nan values:

TypeError: NaNs were detected in the dataset. Try using pd.isnull to find the problematic values.

It seems like the function is not ignoring the DataFrame index.
Versions:

Lifelines: 0.25.8
Pandas: 1.1.5

Hi @joshlk, yup looks like a bug. I think the source is formulaic however. Ex:
from formulaic import Formula

design_info = Formula("1")

df = pd.DataFrame(np.arange(5), index=[0, 2, 4, 6, 8])

print(design_info.get_model_matrix(df))

I'll make an issue with them to resolve this. For now, you can either downgrade a version of lifelines, say 0.25.7, (we recently swapped to Formulaic), or do a .reset_index(drop=True) prior to fitting:
sub_data = data[[True, False]*5].reset_index(drop=True)
regr = WeibullAFTFitter()
regr.fit(sub_data, duration_col='duration', event_col='event')

👋 Formulaic just released 2.2 - try an upgrade locally pip install formulaic== 0.2.2 to fix this.


Custom configurations for Vite/Esbuild

Which @angular/* package(s) are relevant/related to the feature request?
No response
Description
In webpack projects we can use custom configurations adding the builder of https://www.npmjs.com/package/@angular-builders/custom-webpack such as:

Remove unused CSS with PurgeCSS (very useful when using external css libraries like bootstrap)
Move the JS files to a external CDN and modify the urls of index.html and runtime.js to this external CDN
More modifications to styles, javascript files and index.html files

Proposed solution
Add the hability to customize builds of EsBuild and Vite and external plugins
Alternatives considered
Add more properties to angular.json to add keys of customization of esbuild and vite

I'd like this too, I'm using @svgr/webpack today and would need to use esbuild-plugin-svgr with esbuild.

The package referenced above (@angular-builders/custom-webpack) is a third-party package.  The Angular team does not maintain or otherwise support the package.  If you are interested in that project creating a similar package for the new application builder, please consider opening a feature request with that project.  Programmatic APIs within the Angular CLI are available to allow for the creation of such a package with similar functionality.


Fix document filter presenter previous/next URL

This commit adds a new previous/next URL to the document filter presenter that always points to the “web” (human-readable) version of the page rather than being context-driven. Currently, this is a JSON URL when called from the frontend JavaScript which means the previous/next buttons on the relevant finders point to JSON URLs.
Trello: https://trello.com/c/qmKw5mOK/420-fix-whitehall-finders-paginating-to-json-when-changing-filters

Thanks @alextea for notifying us about this bug!


Update  Question 55 README.md

change "which" to "whose"
and added "a" infront of capital letters

@Benappiahpoku  Thanks for PR

Thank you very much


[BUG] Unknown aggregation type [cumulative_cardinality]

Describe the bug
I'm not able to use cumulative_cardinality aggregation in Opensearch
Related component
Search:Aggregations
To Reproduce

Go to '...'
Click on '....'
Scroll down to '....'
See error

Expected behavior
It should provide the response as per aggregation
Additional Details
Plugins
Please list all plugins currently enabled.
Screenshots
If applicable, add screenshots to help explain your problem.
Host/Environment (please complete the following information):

OS: [e.g. iOS]
Version [e.g. 22]

Additional context
Add any other context about the problem here.

[Triage - attendees 1 2 3 4 5 6 7 8]
@tushar-koshti Thanks for creating this issue; however, it isn't being accepted due to not having clear reproduction steps - doesn't seem like a bug. Please feel free to open a new issue after addressing the reason.
It looks like this is a support focused question, please use https://forum.opensearch.org/ for help using features.

@tushar-koshti Feel free to open a feature request issue if you'd like to have support for a new aggregation, but please be specific about what problem you're trying to solve.

Cumulative cardinality aggregation are not supported as of yet in OS. You can open a feature request with use cases that you would like to get supported.


Group Anagrams

I would like to work upon this issue.
Question- Given an array of strings s, group the anagrams together. You can return the answer in any order.
Language- C++

You can start working on this issue. All the best!


fix #102: / in exprs and warn about bad tokens

Coverage remained the same at 86.694% when pulling 365710384aa15a7b70315e9c9e7883f9eeaf2cf6 on fix-102 into cc1b05dd01893677f5c82f04c4d1f0066fe4dac1 on master.


usb_cam_hardware not performing well as claimed

I have run both usb_cam and usb_cam_hardware in Xilinx KRIA KV 260 board (Ubuntu 20.04 and ROS noetic). But I couldn't see lesser CPU utilization as you claimed.
what could be the possible reason for that?

As written in README, you have to publish raw packets from the camera to get 1/10 CPU usage. In other words, only when you use PacketController, you get less CPU usage.


Async Impl

[x] Add callback definitions
[ ] Add callbacks to C wrappers

[x] add extra parameter callback to existed functions or add new functions? new functions, e.g., CvStatus Mat_New_Async(MatCallback callback);
[ ] core
[x] calib3d
[ ] contrib
[x] dnn
[x] features2d
[ ] gapi
[ ] highgui
[x] imgproc
[x] imgcodecs
[x] objdetect
[x] photo
[x] stitching
[x] svd
[x] video

[ ] Add async version of dart code

[x] TODO: new library or mix to current?
[ ] core
[x] calib3d
[ ] contrib
[x] dnn
[x] features2d
[ ] gapi
[ ] highgui
[x] imgproc
[x] imgcodecs
[x] objdetect
[x] photo
[x] stitching
[x] svd
[x] video

[ ] Add async tests

[ ] core
[x] calib3d
[ ] contrib
[x] dnn
[x] features2d
[ ] gapi
[ ] highgui
[x] imgproc
[x] imgcodecs
[x] objdetect
[x] photo
[x] stitching
[x] svd
[x] video

[ ] bump opencv.full to 4.10.0+3

So it works, but just need to rewrite nearly every API.
https://github.com/rainyl/opencv_dart/blob/03ee7e659a294cf28031ad4b76e02b0724ca0b75/example/lib/main.dart#L46-L53

Codecov Report
Attention: Patch coverage is 84.22053% with 83 lines in your changes missing coverage. Please review.

Project coverage is 89.41%. Comparing base (b16eb1b) to head (aaf29a3).

Files
Patch %
Lines

lib/src/gapi/gcomputation.dart
28.57%
25 Missing :warning:

lib/src/core/size.dart
58.00%
21 Missing :warning:

lib/src/core/termcriteria.dart
63.63%
8 Missing :warning:

lib/src/gapi/gmat.dart
61.11%
7 Missing :warning:

lib/src/gapi/gscalar.dart
66.66%
7 Missing :warning:

lib/src/imgproc/imgproc.dart
89.58%
5 Missing :warning:

lib/src/dnn/dnn.dart
89.28%
3 Missing :warning:

lib/src/core/core.dart
85.71%
2 Missing :warning:

lib/src/core/rect.dart
80.00%
2 Missing :warning:

lib/src/video/videoio.dart
33.33%
2 Missing :warning:

... and 1 more

:exclamation: Your organization needs to install the Codecov GitHub app to enable full functionality.
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #101      +/-   ##
==========================================
- Coverage   90.36%   89.41%   -0.95%
==========================================
  Files          35       39       +4
  Lines        5322     5510     +188
==========================================
+ Hits         4809     4927     +118
- Misses        513      583      +70

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

i just saw it, i will retry to implement what i can and open a pr to this pr branch, can we spilt the modules so i handle some and you handle some to avoid we both implementing the same things?

i just saw it, i will try to implement what i can and open a pr to this pr branch, can we spilt the modules so i handle some and you handle some to avoid we both implementing the same things?

Sure, just create a new branch from async branch

also whats the easiest module i can follow as a reference since this pr has the alot of changes, so an easy module to follow will be the best option

For now I just implemented calib3d and imgcodecs, I think imgcodecs is the easiest, just several API in it, but remember to take a loot at core/types.h, in which many basic definitions inside it.

@abdelaziz-mahdy I have added async version of SVD, hope you are not doing the same module, may I ask which module are you working (or planning working) on?

I think dnn or objdetect, and if I faced any problem will let you know

can i ask why is this removed?https://github.com/rainyl/opencv_dart/pull/101/commits/b077b4a63ae6a9999a86557afda9e994848c4f4f i thought it will make it easier on us.

can i ask why is this removed?b077b4a i thought it will make it easier on us.

It's duplicate, https://github.com/rainyl/opencv_dart/blob/b077b4a63ae6a9999a86557afda9e994848c4f4f/lib/src/core/base.dart#L203-L207

can i ask why is this removed?b077b4a i thought it will make it easier on us.

It's duplicated,
https://github.com/rainyl/opencv_dart/blob/b077b4a63ae6a9999a86557afda9e994848c4f4f/lib/src/core/base.dart#L203-L207

very weird since i couldnt find it, maybe it was added in another commit, peace

@abdelaziz-mahdy I think it's time to merge, thanks for your efforts!

@abdelaziz-mahdy I think it's time to merge, thanks for your efforts!

Thank you for everything 💖


[Errno 2] No such file or directory: 'stylegan2-ffhq-config-f.pt'

error in colab
[Errno 2] No such file or directory: 'stylegan2-ffhq-config-f.pt'
from main import main
from argparse import Namespace
result = main(Namespace(**args))

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-4-fbc1a59be2c9> in <module>()
      1 from main import main
      2 from argparse import Namespace
----> 3 result = main(Namespace(**args))

3 frames
/usr/local/lib/python3.6/dist-packages/torch/serialization.py in __init__(self, name, mode)
    209 class _open_file(_opener):
    210     def __init__(self, name, mode):
--> 211         super(_open_file, self).__init__(open(name, mode))
    212
    213     def __exit__(self, *args):

FileNotFoundError: [Errno 2] No such file or directory: 'stylegan2-ffhq-config-f.pt'

found out there is no permission to download from drive
Permission denied: https://drive.google.com/uc?id=1EM87UquaoQmk17Q8d5kYIAHqu0dkYqdT
Maybe you need to change permission over 'Anyone with the link'?

Yes, the Google Drive quota has been reached.

Try this:

for PyTorch: https://nvlabs-fi-cdn.nvidia.com/stylegan2-ada-pytorch/pretrained/transfer-learning-source-nets/ffhq-res1024-mirror-stylegan2-noaug.pkl
for TensforFlow 1: https://nvlabs-fi-cdn.nvidia.com/stylegan2-ada/pretrained/transfer-learning-source-nets/ffhq-res1024-mirror-stylegan2-noaug.pkl

You can also try using PyDrive, it worked for me:
from pydrive.auth import GoogleAuth
from pydrive.drive import GoogleDrive
from google.colab import auth
from oauth2client.client import GoogleCredentials

# Authenticate and create the PyDrive client.
auth.authenticate_user()
gauth = GoogleAuth()
gauth.credentials = GoogleCredentials.get_application_default()
drive = GoogleDrive(gauth)

file_id = '1EM87UquaoQmk17Q8d5kYIAHqu0dkYqdT'
downloaded = drive.CreateFile({'id':file_id})
downloaded.FetchMetadata(fetch_all=True)
downloaded.GetContentFile(downloaded.metadata['title'])

Thanks @woctezuma and @ramtiin !
@molo32 please close the issue if the problem is solved, and let me know if you need further help

Issue persists.
The file should either be hosted somewhere without those traffic limits, or the code should be modified to use something like PyDrive as that seems to work for @ramtiin.

Hi @n00mkrad ,
I can reproduce the problem, but I change the code so that it will use the solution that worked for @ramtiin .
Can you check if it solves the problem?

Works now.

cool


v3.7.0 is a breaking change

Version 3.7.0 is a breaking change. Does this project follow semver? If not, I'll pin my project to use 3.6.0 until 3.7.0 is fixed (see https://github.com/actions/setup-node/issues/797#issuecomment-1640885997).
If this was not meant to be a breaking change, I suggest unpublishing version 3.7.0 or doing a patch version to revert functionality

Hello @eddiemonge. Thank you for your report. I think it is not a breaking change because regarding to the thread it didn't work as expected initially because of parsing logic that is why on the post step the action was getting different value.

Changing the default or expected value from null to string would seem to me to be breaking. One day my gh actions worked, and the next, they didn't, without my code changing. I would consider that a breaking change, since it had been that way all of 3.x

Could you please describe your case with changing value from null to string? Do you mean post input or what ?

Hello @eddiemonge. Could you please try to use changes changes from the main branch ?

Hello @eddiemonge. The new versions of setup-node was released. For now I'm going to close the issue.


kubelet/containerd logs "failed to setup network for sandbox" when using istio-cni 1.9.3 on CentOS7

(NOTE: This is used to report product bugs:
To report a security vulnerability, please visit https://istio.io/about/security-vulnerabilities
To ask questions about how to use Istio, please visit https://discuss.istio.io)
Bug description
This is a continuation of a slack thread. In my cluster, as the nodes get busier, istio-proxy-injected pods take longer to start (and sometimes can't start at all), with kubelet/container messages about failed to setup network for sandbox. The pods do eventually start, given enough time.
[ ] Docs
[ ] Installation
[X] Networking
[ ] Performance and Scalability
[ ] Extensions and Telemetry
[ ] Security
[ ] Test and Release
[ ] User Experience
[ ] Developer Infrastructure
[ ] Upgrade
Expected behavior
When using istio-cni, pods should start up normally
Steps to reproduce the bug

Install istio with cni.enabled (my cluster is kubeadm-built, on CentOS7 using kernel 5.11)
Create a namespace with 'istio-injection=enabled' label applied (I called mine "sandbox")
Create a simple deployment in this namespace (kubectl create deployment -n sandbox --image=nginx test)
Scale the deployment up enough to make the nodes work a bit
Observe the kubelet logs, and describe the created pods. You'll note events like this:

Events:
  Type     Reason                  Age    From               Message
  ----     ------                  ----   ----               -------
  Normal   Scheduled               3m11s  default-scheduler  Successfully assigned sandbox/test-5f6778868d-28hnw to cow1
  Warning  FailedCreatePodSandBox  3m10s  kubelet            Failed to create pod sandbox: rpc error: code = Unknown desc = failed to setup network for sandbox "fb4d0911dadea4690e006ab393bb42ebc1547cca154e74dddc9ccefdec81a38d": exit status 2
  Warning  FailedCreatePodSandBox  3m8s   kubelet            Failed to create pod sandbox: rpc error: code = Unknown desc = failed to setup network for sandbox "7bab640fc109d1d4d9727c44d96df1847d56bad738e6f39616a9a0a859cf145b": exit status 2
  Normal   Pulling                 3m7s   kubelet            Pulling image "gergorg/proxyv2:1.9.3"
  Normal   Pulled                  3m7s   kubelet            Successfully pulled image "gergorg/proxyv2:1.9.3" in 752.672805ms
  Normal   Created                 3m7s   kubelet            Created container istio-validation
  Normal   Started                 3m6s   kubelet            Started container istio-validation
  Normal   Pulling                 3m6s   kubelet            Pulling image "gergorg/proxyv2:1.9.3"
  Normal   Pulled                  3m5s   kubelet            Successfully pulled image "gergorg/proxyv2:1.9.3" in 788.467888ms

Version (include the output of istioctl version --remote and kubectl version --short and helm version --short if you used Helm)
root@cowboy:~# istioctl version --remote
client version: 1.9.3
control plane version: 1.9.3
data plane version: 1.9.3 (156 proxies), 1.9.0 (26 proxies)
root@cowboy:~# kubectl version --short
Client Version: v1.20.5
Server Version: v1.20.5
root@cowboy:~# helm version --short
v3.5.4+g1b5edb6
root@cowboy:~#

How was Istio installed?
Using istio-operator, which was installed by helm
Environment where the bug was observed (cloud vendor, OS, etc)
Bare-metal cluster created with kubeadm, using Calico 3.19 as a CNI
Additionally, please consider running istioctl bug-report and attach the generated cluster-state tarball to this issue.
Refer cluster state archive for more details (I opted not to do this yet, since I'm not sure whether the data created in the bug report may contain confidential information)
Debug logs from kubelet on one of the nodes are here:
debug-logs-cow1.log

Here's the conflist file requested :)
conflist.txt

Was this confirmed to be a result of Istio CNI?
Meaning was it confirmed that cluster set ups without Istio or perhaps just without Istio CNI being used do not reproduce this behavior?
If there is more information which directly correlates these observations to Istio CNI, please share.
FYI, we are also observing same reported symptoms on GKE 1.18 & 1.19 (their container optimized OS), containerD & Docker runtimes and those were using Calico 3.16. We had observed failure to create sandbox errors in previous cluster builds (Istio < 1.9.x), but our latest upgrades seem to produce the errors significantly more. These upgrades included moving to GKE 1.19 and to Istio 1.9.2 among other functional changes.

This is likely due to https://github.com/istio/istio/issues/31936. For istio <= 1.10, istio-cni will only run iptables once, and if it gets xtables lock failure, it exists with code 2. At istio 1.11, this should be improved a bit since we added retry. However, it still won't help if the node is super busy and xtables lock is always hold..


Design QA - My Bets Tooltip over Outcome

This tooltip should appear when you hover the outcome. Right now the position doesn't seem right.
The tooltip shouldn't appear if there is enough room for the outcome name. So, I think in this particular case, I shouldn't see at all.

Looks fine on big resolutions, but it's not working fine on smaller ones:

Figma reference:
https://www.figma.com/file/wogMuUDylgOHgTEYhZ3jgp/Augur-Bet-UI?node-id=7654%3A268226

seems with a 32 limit character count the tooltip won't show anyway


Validate base surveys using Base64

JIRA: https://projects.engineering.redhat.com/browse/SSP-837

@eclarizio @mkanoor could you take another look at this?

@eclarizio applied the last feedback please take a look again?


Fix test script not running on Windows environments

Summary
Trying to run our tests on a Windows environment returns the error 'BABEL_ENV' is not recognized as an internal or external command. Using cross-env should fix it.
Image as reference by @emidev98:

Were you able to test this on a Windows environment?

Were you able to test this on a Windows environment?

@sponglord Yes, it works fine.

@sponglord Yes, it works fine.


Allow module without version

PR Summary
Allow modules that don't have a version directory to be added in $env:PSModulePath.
PR Context
The Get-DscResourceModules function scans the $env:PSModulePath to find relevant modules to be included in the cache. When a module doesn't have a version directory, it does not find the module. This change allows the ability to include modules that don't contain the directory.
I added this change because it can be useful for testing purposes to see the participation of DSC resources when developing them. For example, take the winget-dsc repository. Simply adding the resource to the environment variable adds it for participation.

Added the OTBS to the settings.json file. It might help other folks in the future when they are working with the PowerShell scripts. All remarks resolved @SteveL-MSFT


chore(deps): upgrade dev dependencies

Upgrades project dependencies. See details in workflow run.

Automatically created by projen via the "upgrade-dev-dependencies-k8s-28-main" workflow

⚪ Backport skipped
The pull request was not backported as there were no branches to backport to. If this is a mistake, please apply the desired version labels or run the backport tool manually.
Manual backport
To create the backport manually run:
backport --pr 4062

Questions ?
Please refer to the Backport tool documentation


reference genomes

Hi, I was wondering if you are considering to open nanome to other references ? Basically, I've been running most of the tools you have included in nanome on my datasets/references but separately. Therefore, it would really help to have a tool such nanome for it.
Thank you,
Best Regards
P

Thank you for this suggestion. Supporting all other types of reference genome will be a very important feature for our pipeline. I will open other reference genome in recent and let you know.
Best regard,
Yang

This function has been merged into master, check documents here: https://github.com/TheJacksonLaboratory/nanome/blob/master/docs/SpecificUsage.md#1-how-to-use-other-reference-genome-in-nanome

Thank you very much for this. I'm going to test it and I'll let you know

Hi, I've tested with my own data and it works well (using cpu mode for basecall). However, I noticed that it does not detect my GPU. I've manually exported cuda device (export CUDA_VISIBLE_DEVICES=0) but then, using docker I get:
"CUDA error at /builds/ofan/ont_core_cpp/ont_core/common/cuda_common.cpp:203: CUDA_ERROR_NO_DEVICE"
and using singularity:
"CUDA error at /builds/ofan/ont_core_cpp/ont_core/common/cuda_common.cpp:203: CUDA_ERROR_SYSTEM_DRIVER_MISMATCH
any hints? Outside the containers gpu guppy basecall works well.
thanx

Hi,
User do not need to export CUDA_VISIBLE_DEVICES again. If your computer system have GPU, the variable should be visible to pipeline, and the pipeline will automatically use GPU command options.
The CUDA_ERROR_NO_DEVICE means your system do not have GPU devices, but you have provided CUDA_VISIBLE_DEVICES. The CUDA_ERROR_SYSTEM_DRIVER_MISMATCH  means your CUDA device (not V100 or P100) is not compatible with cuda library installed in default container, in this case, you have to build your container.
Would you please rerun below command to test GPU running on your platform?
nvcc --version

nvidia-smi

nextflow run main.nf -profile test,singularity

Please check which process failed, for example, if process [c1/47c145] process > Basecall failed, you can dive into folder `work/c1/47c145*' to check more detailed errors, and even rerun that command.
Also you can post the .nextflow.log and the error command log file here, in order for me to further check your problem.

Hi, first of all, thank you a lot for your prompt feedback. Regarding your questions/comments, I must say that I'm testing your pipeline (as I do with many) in a small workstation with the following config:
System:    Kernel: 5.4.0-96-generic x86_64 bits: 64 compiler: gcc v: 9.3.0 Desktop: Cinnamon 5.2.7
wm: muffin dm: LightDM Distro: Linux Mint 20.3 Una base: Ubuntu 20.04 focal
CPU:       Topology: 12-Core model: AMD Ryzen Threadripper 2920X bits: 64 type: MT MCP arch: Zen+
rev: 2 L2 cache: 6144 KiB
Graphics:  Device-1: NVIDIA vendor: ASUSTeK driver: nvidia v: 510.39.01 bus ID: 42:00.0
chip ID: 10de:2484
Display: x11 server: X.Org 1.20.13 driver: nvidia
unloaded: fbdev,modesetting,nouveau,vesa resolution: 2560x1440~144Hz
OpenGL: renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2 v: 4.6.0 NVIDIA 510.39.01
nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2021 NVIDIA Corporation
Built on Fri_Dec_17_18:16:03_PST_2021
Cuda compilation tools, release 11.6, V11.6.55
Build cuda_11.6.r11.6/compiler.30794723_0
nvidia-smi
| NVIDIA-SMI 510.39.01    Driver Version: 510.39.01    CUDA Version: 11.6     |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|                               |                      |               MIG M. |
|===============================+======================+======================|
|   0  NVIDIA GeForce ...  On   | 00000000:42:00.0  On |                  N/A |
|  0%   25C    P8    22W / 220W |    461MiB /  8192MiB |      0%      Default |
|                               |                      |                  N/A |
nextflow run main.nf -profile test,singularity
N E X T F L O W  ~  version 21.10.6
Not a valid project name: main.nf
running (without manually exporting CUDA_VISIBLE_DEVICES): nextflow run TheJacksonLaboratory/nanome -profile test,singularity
N E X T F L O W  ~  version 21.10.6
Launching TheJacksonLaboratory/nanome [deadly_volhard] - revision: a1849cb763 [master]
NANOME - NF PIPELINE (v1.3.7)
by Li Lab at The Jackson Laboratory
https://github.com/TheJacksonLaboratory/nanome
dsname              : CIEcoli
input               : https://github.com/TheJacksonLaboratory/nanome/raw/master/test_data/ecoli_ci_test_fast5.tar.gz
genome              : ecoli - [https://storage.googleapis.com/jax-nanopore-01-project-data/nanome-input/ecoli.tar.gz]
Running settings   : --------
processors          : 2
chrSet              : NC_000913.3
dataType            : ecoli
runBasecall         : Yes
runNanopolish       : Yes
runDeepSignal       : Yes
runGuppy            : Yes
runTombo            : Yes
runDeepMod          : Yes
runNANOME           : Yes
outputRaw           : true
Model summary      : --------
GUPPY_BASECALL_MODEL: dna_r9.4.1_450bps_hac.cfg
DEEPSIGNAL_MODEL_DIR/DEEPSIGNAL_MODEL: model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+/bn_17.sn_360.epoch_9.ckpt
GUPPY_METHCALL_MODEL: dna_r9.4.1_450bps_modbases_5mc_hac.cfg
DEEPMOD_RNN_MODEL   : rnn_conmodC_P100wd21_f7ne1u0_4/mod_train_conmodC_P100wd21_f3ne1u0
=================================
executor >  local (16)
[c6/8a705d] process > EnvCheck (CIEcoli)                   [100%] 1 of 1 ✔
[8a/5bffcd] process > Untar (ecoli_ci_test_fast5.tar)      [100%] 1 of 1 ✔
[ba/2952e6] process > Basecall (ecoli_ci_test_fast5.tar)   [100%] 1 of 1 ✔
[50/4fc66d] process > QCExport (CIEcoli)                   [100%] 1 of 1 ✔
[cf/0eda03] process > Resquiggle (ecoli_ci_test_fast5.tar) [100%] 1 of 1 ✔
[78/1d92a2] process > Nanopolish (ecoli_ci_test_fast5.tar) [100%] 1 of 1 ✔
[15/2ab5bd] process > NplshComb (CIEcoli)                  [100%] 1 of 1 ✔
[f5/1d1786] process > DeepSignal (ecoli_ci_test_fast5.tar) [100%] 1 of 1 ✔
[d6/1eea5a] process > DpSigComb (CIEcoli)                  [100%] 1 of 1 ✔
[b8/df2702] process > Guppy (ecoli_ci_test_fast5.tar)      [100%] 1 of 1 ✔
[67/cbb8b8] process > GuppyComb (CIEcoli)                  [100%] 1 of 1 ✔
[27/cef4dc] process > Tombo (ecoli_ci_test_fast5.tar)      [100%] 1 of 1 ✔
[ca/0cc5ff] process > TomboComb (CIEcoli)                  [100%] 1 of 1 ✔
[a4/9ad71f] process > DeepMod (ecoli_ci_test_fast5.tar)    [100%] 1 of 1 ✔
[13/e907a0] process > DpmodComb (CIEcoli)                  [100%] 1 of 1 ✔
[41/edfc19] process > Report (CIEcoli)                     [100%] 1 of 1 ✔
Completed at: 29-Jan-2022 14:48:46
Duration    : 1m 26s
CPU hours   : (a few seconds)
Succeeded   : 16
But when checking the Basecall process command.log I can see :
CUDA_VISIBLE_DEVICES=
Detect no GPU, using CPU commandType
/usr/bin/guppy_basecaller
: Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 5.0.16+b9fcd7b5b
So, if I add to .bashrc "export CUDA_VISIBLE_DEVICES=0" (which should not be needed), I get:
[ca/10a27b] process > EnvCheck (CIEcoli)                 [100%] 1 of 1 ✔
[a2/ff08a2] process > Untar (ecoli_ci_test_fast5.tar)    [100%] 1 of 1 ✔
[9f/bb0333] process > Basecall (ecoli_ci_test_fast5.tar) [100%] 1 of 1, failed: 1 ✔
[-        ] process > QCExport                           -
[-        ] process > Resquiggle                         -
[-        ] process > Nanopolish                         -
[-        ] process > NplshComb                          -
[-        ] process > DeepSignal                         -
[-        ] process > DpSigComb                          -
[41/ba8620] process > Guppy (ecoli_ci_test_fast5.tar)    [100%] 1 of 1, failed: 1 ✔
[-        ] process > GuppyComb                          -
[-        ] process > Tombo                              -
[-        ] process > TomboComb                          -
[-        ] process > DeepMod                            -
[-        ] process > DpmodComb                          -
[-        ] process > Report                             -
Staging foreign file: https://github.com/TheJacksonLaboratory/nanome/raw/master/test_data/ecoli_ci_test_fast5.tar.gz
Pulling Singularity image docker://liuyangzzu/nanome:v1.3 [cache /home/pedro/Documents/nanopore/211203/local_singularity_cache/liuyangzzu-nanome-v1.3.img]
Staging foreign file: https://storage.googleapis.com/jax-nanopore-01-project-data/nanome-input/model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+.tar.gz
[9f/bb0333] NOTE: Process Basecall (ecoli_ci_test_fast5.tar) terminated with an error exit status (255) -- Error is ignored
[41/ba8620] NOTE: Process Guppy (ecoli_ci_test_fast5.tar) terminated with an error exit status (255) -- Error is ignored
In the Basecall process command.log I can see:
CUDA_VISIBLE_DEVICES=0
Detect GPU, using GPU commandType
/usr/bin/guppy_basecaller
: Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 5.0.16+b9fcd7b5b
but also (CIEcoli.ecoli_ci_test_fast5.tar.Basecall.run.log):
ONT Guppy basecalling software version 5.0.16+b9fcd7b5b
config file:        /opt/ont/guppy/data/dna_r9.4.1_450bps_hac.cfg
model file:         /opt/ont/guppy/data/template_r9.4.1_450bps_hac.jsn
input path:         ecoli_ci_test_fast5.tar.untar
save path:          ecoli_ci_test_fast5.tar.basecalled
chunk size:         2000
chunks per runner:  256
minimum qscore:     9
records per file:   4000
fastq compression:  ON
num basecallers:    1
gpu device:         auto
kernel path:
runners per device: 4
[guppy/error] main: CUDA error at /builds/ofan/ont_core_cpp/ont_core/common/cuda_common.cpp:203: CUDA error at /builds/ofan/ont_core_cpp/ont_core/common/cuda_common.cpp:203: CUDA_ERROR_SYSTEM_DRIVER_MISMATCH
[guppy/warning] main: An error has occurred. Aborting.
The nextflow.log:
Jan-29 15:03:59.130 [main] DEBUG nextflow.cli.Launcher - $> nextflow run TheJacksonLaboratory/nanome -profile test,singularity
Jan-29 15:03:59.172 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 21.10.6
Jan-29 15:04:00.197 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/.git/config; branch: master; remote: origin; url: https://github.com/TheJacksonLaboratory/nanome.git
Jan-29 15:04:00.209 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/.git/config; branch: master; remote: origin; url: https://github.com/TheJacksonLaboratory/nanome.git
Jan-29 15:04:00.286 [main] INFO  nextflow.cli.CmdRun - Launching TheJacksonLaboratory/nanome [trusting_stonebraker] - revision: a1849cb763 [master]
Jan-29 15:04:00.873 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/nextflow.config
Jan-29 15:04:00.874 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/nextflow.config
Jan-29 15:04:00.879 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: test,singularity
Jan-29 15:04:01.136 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, sumner, test, conda, winter, singularity, hpc, google, test_human, docker]
Jan-29 15:04:01.162 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/pedro/.nextflow/plugins
Jan-29 15:04:01.163 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jan-29 15:04:01.172 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jan-29 15:04:01.173 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jan-29 15:04:01.176 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jan-29 15:04:01.184 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jan-29 15:04:01.234 [main] DEBUG nextflow.Session - Session uuid: 631a06e9-8fb1-4e64-917f-0f2a5c74e477
Jan-29 15:04:01.234 [main] DEBUG nextflow.Session - Run name: trusting_stonebraker
Jan-29 15:04:01.234 [main] DEBUG nextflow.Session - Executor pool size: 24
Jan-29 15:04:01.258 [main] DEBUG nextflow.cli.CmdRun -
Version: 21.10.6 build 5660
Created: 21-12-2021 16:55 UTC (16:55 WEST)
System: Linux 5.4.0-96-generic
Runtime: Groovy 3.0.9 on OpenJDK 64-Bit Server VM 11.0.13+8-Ubuntu-0ubuntu1.20.04
Encoding: UTF-8 (UTF-8)
Process: 39052@ryzen [<IP_ADDRESS>]
CPUs: 24 - Mem: 125.7 GB (108.8 GB) - Swap: 112.7 GB (112.7 GB)
Jan-29 15:04:01.273 [main] DEBUG nextflow.Session - Work-dir: /home/pedro/Documents/nanopore/211203/work [ext2/ext3]
Jan-29 15:04:01.273 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/bin
Jan-29 15:04:01.281 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jan-29 15:04:01.292 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jan-29 15:04:01.384 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 25; maxThreads: 1000
Jan-29 15:04:01.452 [main] DEBUG nextflow.Session - Session start invoked
Jan-29 15:04:03.593 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jan-29 15:04:03.646 [main] INFO  nextflow.Nextflow - NANOME - NF PIPELINE (v1.3.7)
by Li Lab at The Jackson Laboratory
https://github.com/TheJacksonLaboratory/nanome
Jan-29 15:04:03.648 [main] INFO  nextflow.Nextflow - dsname              : CIEcoli
input               : https://github.com/TheJacksonLaboratory/nanome/raw/master/test_data/ecoli_ci_test_fast5.tar.gz
genome              : ecoli - [https://storage.googleapis.com/jax-nanopore-01-project-data/nanome-input/ecoli.tar.gz]
Running settings   : --------
processors          : 2
chrSet              : NC_000913.3
dataType            : ecoli
runBasecall         : Yes
runNanopolish       : Yes
runDeepSignal       : Yes
runGuppy            : Yes
runTombo            : Yes
runDeepMod          : Yes
runNANOME           : Yes
outputRaw           : true
Model summary      : --------
GUPPY_BASECALL_MODEL: dna_r9.4.1_450bps_hac.cfg
DEEPSIGNAL_MODEL_DIR/DEEPSIGNAL_MODEL: model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+/bn_17.sn_360.epoch_9.ckpt
GUPPY_METHCALL_MODEL: dna_r9.4.1_450bps_modbases_5mc_hac.cfg
DEEPMOD_RNN_MODEL   : rnn_conmodC_P100wd21_f7ne1u0_4/mod_train_conmodC_P100wd21_f3ne1u0
Pipeline settings  : --------
Working dir         : /home/pedro/Documents/nanopore/211203/work
Output dir          : results
Launch dir          : /home/pedro/Documents/nanopore/211203
Script dir          : /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome
User                : pedro
Profile             : test,singularity
Config files        : /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/nextflow.config
Pipeline Release    : master
Container           : singularity - docker://liuyangzzu/nanome:v1.3
errorStrategy       : ignore
maxRetries          : 5
Jan-29 15:04:03.649 [main] INFO  nextflow.Nextflow - =================================
Jan-29 15:04:04.006 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:EnvCheck matches process EnvCheck
Jan-29 15:04:04.011 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.011 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.015 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jan-29 15:04:04.020 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=24; memory=125.7 GB; capacity=50; pollInterval=100ms; dumpInterval=5m
Jan-29 15:04:04.041 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 25; maxThreads: 1000
Jan-29 15:04:04.094 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.094 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.100 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.101 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.124 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.124 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.134 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.134 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.146 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1]
Jan-29 15:04:04.153 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.153 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.156 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1]
Jan-29 15:04:04.163 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.163 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.172 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.172 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.176 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1, 2]
Jan-29 15:04:04.184 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.185 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.196 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.196 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.199 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1, 2]
Jan-29 15:04:04.218 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.218 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.224 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.224 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.226 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1]
Jan-29 15:04:04.233 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.234 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.239 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.239 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.241 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1]
Jan-29 15:04:04.250 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.250 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.275 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.275 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.284 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: EnvCheck, Report, METEORE, QCExport, DpSigComb, Basecall, GuppyComb, Tombo, NewTool, Untar, Resquiggle, DeepMod, NewToolComb, Nanopolish, Guppy, DpmodComb, NplshComb, TomboComb, Megalodon, DeepSignal, MgldnComb
Jan-29 15:04:04.285 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Jan-29 15:04:04.287 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Jan-29 15:04:04.288 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Jan-29 15:04:04.288 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Jan-29 15:04:04.288 [main] DEBUG nextflow.Session - Ignite dataflow network (38)
Jan-29 15:04:04.295 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > EnvCheck
Jan-29 15:04:04.296 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Untar
Jan-29 15:04:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Basecall
Jan-29 15:04:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > QCExport
Jan-29 15:04:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Resquiggle
Jan-29 15:04:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Resquiggle
Jan-29 15:04:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Nanopolish
Jan-29 15:04:04.298 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Nanopolish
Jan-29 15:04:04.298 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NplshComb
Jan-29 15:04:04.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DeepSignal
Jan-29 15:04:04.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DeepSignal
Jan-29 15:04:04.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DpSigComb
Jan-29 15:04:04.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Guppy
Jan-29 15:04:04.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Guppy
Jan-29 15:04:04.302 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GuppyComb
Jan-29 15:04:04.304 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Tombo
Jan-29 15:04:04.305 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Tombo
Jan-29 15:04:04.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TomboComb
Jan-29 15:04:04.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DeepMod
Jan-29 15:04:04.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DeepMod
Jan-29 15:04:04.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DpmodComb
Jan-29 15:04:04.307 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Report
Jan-29 15:04:04.308 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Jan-29 15:04:04.308 [main] DEBUG nextflow.Session - Session await
Jan-29 15:04:05.491 [Actor Thread 22] DEBUG n.util.BlockingThreadExecutorFactory - Thread pool name=FileTransfer; maxThreads=72; maxQueueSize=216; keepAlive=1m
Jan-29 15:04:05.496 [FileTransfer-thread-1] DEBUG nextflow.file.FilePorter - Copying foreign file https://storage.googleapis.com/jax-nanopore-01-project-data/nanome-input/ecoli.tar.gz to work dir: /home/pedro/Documents/nanopore/211203/work/stage/00/f9f02f36eeefdad0fd371c174a73c7/ecoli.tar.gz
Jan-29 15:04:05.733 [FileTransfer-thread-2] DEBUG nextflow.file.FilePorter - Copying foreign file https://storage.googleapis.com/jax-nanopore-01-project-data/nanome-input/model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+.tar.gz to work dir: /home/pedro/Documents/nanopore/211203/work/stage/17/3f93549f94c98aadaa33abe75ec1ca/model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+.tar.gz
Jan-29 15:04:05.947 [FileTransfer-thread-3] DEBUG nextflow.file.FilePorter - Copying foreign file https://github.com/TheJacksonLaboratory/nanome/raw/master/test_data/ecoli_ci_test_fast5.tar.gz to work dir: /home/pedro/Documents/nanopore/211203/work/stage/ac/7bdceb3a0dddc741c890ed4c479338/ecoli_ci_test_fast5.tar.gz
Jan-29 15:04:07.947 [Actor Thread 25] INFO  nextflow.file.FilePorter - Staging foreign file: https://github.com/TheJacksonLaboratory/nanome/raw/master/test_data/ecoli_ci_test_fast5.tar.gz
Jan-29 15:04:08.206 [Actor Thread 20] INFO  nextflow.container.SingularityCache - Pulling Singularity image docker://liuyangzzu/nanome:v1.3 [cache /home/pedro/Documents/nanopore/211203/local_singularity_cache/liuyangzzu-nanome-v1.3.img]
Jan-29 15:04:08.891 [Actor Thread 22] INFO  nextflow.file.FilePorter - Staging foreign file: https://storage.googleapis.com/jax-nanopore-01-project-data/nanome-input/model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+.tar.gz
Jan-29 15:04:12.191 [Actor Thread 20] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=docker://liuyangzzu/nanome:v1.3 path=/home/pedro/Documents/nanopore/211203/local_singularity_cache/liuyangzzu-nanome-v1.3.img
Jan-29 15:04:12.282 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 15:04:12.286 [Task submitter] INFO  nextflow.Session - [a2/ff08a2] Submitted process > Untar (ecoli_ci_test_fast5.tar)
Jan-29 15:04:12.790 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: Untar (ecoli_ci_test_fast5.tar); status: COMPLETED; exit: 0; error: -; workDir: /home/pedro/Documents/nanopore/211203/work/a2/ff08a2905c3972cc682b51622b44ed]
Jan-29 15:04:12.842 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 15:04:12.843 [Task submitter] INFO  nextflow.Session - [9f/bb0333] Submitted process > Basecall (ecoli_ci_test_fast5.tar)
Jan-29 15:04:14.226 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: Basecall (ecoli_ci_test_fast5.tar); status: COMPLETED; exit: 255; error: -; workDir: /home/pedro/Documents/nanopore/211203/work/9f/bb0333f896fb508bd348bc98bc830e]
Jan-29 15:04:14.234 [Task monitor] INFO  nextflow.processor.TaskProcessor - [9f/bb0333] NOTE: Process Basecall (ecoli_ci_test_fast5.tar) terminated with an error exit status (255) -- Error is ignored
Jan-29 15:04:28.441 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/null1
Jan-29 15:04:28.444 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/validate_nanome_container.sh
Jan-29 15:04:28.444 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/gcf52ref.patch
Jan-29 15:04:28.444 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/sum_chr_mod.py
Jan-29 15:04:28.444 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/clean_old_basecall_in_fast5.py
Jan-29 15:04:28.444 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/combination_model_prediction.py
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/unify_format_for_calls.sh
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/null3
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/preindexing_check_dups.py
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/hm_cluster_predict.py
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/gcf52ref.tar.gz
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/null2
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/extract_methylation_fast5_support_dir.py
Jan-29 15:04:28.446 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/tombo_extract_per_read_stats.py
Jan-29 15:04:28.446 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/FilesSeparator.sh
Jan-29 15:04:28.446 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/FilesSeparator.py
Jan-29 15:04:28.454 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 15:04:28.455 [Task submitter] INFO  nextflow.Session - [ca/10a27b] Submitted process > EnvCheck (CIEcoli)
Jan-29 15:04:38.309 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: EnvCheck (CIEcoli); status: COMPLETED; exit: 0; error: -; workDir: /home/pedro/Documents/nanopore/211203/work/ca/10a27b848b85590e50e99c47fc4839]
Jan-29 15:04:38.310 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process EnvCheck (CIEcoli) is unable to find [UnixPath]: /home/pedro/Documents/nanopore/211203/work/ca/10a27b848b85590e50e99c47fc4839/rerio (pattern: rerio)
Jan-29 15:04:38.378 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process EnvCheck > Skipping output binding because one or more optional files are missing: fileoutparam<1>
Jan-29 15:04:38.453 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 15:04:38.454 [Task submitter] INFO  nextflow.Session - [41/ba8620] Submitted process > Guppy (ecoli_ci_test_fast5.tar)
Jan-29 15:04:39.813 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: Guppy (ecoli_ci_test_fast5.tar); status: COMPLETED; exit: 255; error: -; workDir: /home/pedro/Documents/nanopore/211203/work/41/ba862049350f4d29c6d65fed9a4830]
Jan-29 15:04:39.814 [Task monitor] INFO  nextflow.processor.TaskProcessor - [41/ba8620] NOTE: Process Guppy (ecoli_ci_test_fast5.tar) terminated with an error exit status (255) -- Error is ignored
Jan-29 15:04:39.817 [main] DEBUG nextflow.Session - Session await > all process finished
Jan-29 15:04:39.913 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jan-29 15:04:39.923 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=2; failedCount=2; ignoredCount=2; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=10.2s; failedDuration=2.6s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=0; ]
Jan-29 15:04:39.949 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
Jan-29 15:04:39.963 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
Outside the container, I can easily resort to cuda for guppy gpu basecalling:
chunk size:         2000
chunks per runner:  512
minimum qscore:     8
records per file:   4000
fastq compression:  ON
num basecallers:    1
gpu device:         cuda:0
kernel path:
runners per device: 4
2022-01-26 15:14:54.506944 [guppy/info] crashpad_handler successfully launched.
2022-01-26 15:14:54.789242 [guppy/info] CUDA device 0 (compute 8.6) initialised, memory limit<PHONE_NUMBER>B<PHONE_NUMBER>B free)
2022-01-26 15:14:55.471325 [guppy/message] Found 428 fast5 files to process.
2022-01-26 15:14:55.485657 [guppy/message] Init time: 977 ms
2022-01-26 15:14:56.542819 [guppy/info] Read '597db6b0-2a75-4d22-8ebe-d354ec6bad3e' from file "FAQ28390_2b9848fd_0.fast5" has been loaded.

Hi, first of all, thank you a lot for your prompt feedback. Regarding your questions/comments, I must say that I'm testing your pipeline (as I do with many) in a small workstation with the following config:
System:    Kernel: 5.4.0-96-generic x86_64 bits: 64 compiler: gcc v: 9.3.0 Desktop: Cinnamon 5.2.7
wm: muffin dm: LightDM Distro: Linux Mint 20.3 Una base: Ubuntu 20.04 focal
CPU:       Topology: 12-Core model: AMD Ryzen Threadripper 2920X bits: 64 type: MT MCP arch: Zen+
rev: 2 L2 cache: 6144 KiB
Graphics:  Device-1: NVIDIA vendor: ASUSTeK driver: nvidia v: 510.39.01 bus ID: 42:00.0
chip ID: 10de:2484
Display: x11 server: X.Org 1.20.13 driver: nvidia
unloaded: fbdev,modesetting,nouveau,vesa resolution: 2560x1440~144Hz
OpenGL: renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2 v: 4.6.0 NVIDIA 510.39.01

nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2021 NVIDIA Corporation
Built on Fri_Dec_17_18:16:03_PST_2021
Cuda compilation tools, release 11.6, V11.6.55
Build cuda_11.6.r11.6/compiler.30794723_0

nvidia-smi
| NVIDIA-SMI 510.39.01    Driver Version: 510.39.01    CUDA Version: 11.6     |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|                               |                      |               MIG M. |
|===============================+======================+======================|
|   0  NVIDIA GeForce ...  On   | 00000000:42:00.0  On |                  N/A |
|  0%   25C    P8    22W / 220W |    461MiB /  8192MiB |      0%      Default |
|                               |                      |                  N/A |

nextflow run main.nf -profile test,singularity
N E X T F L O W  ~  version 21.10.6
Not a valid project name: main.nf

running (without manually exporting CUDA_VISIBLE_DEVICES): nextflow run TheJacksonLaboratory/nanome -profile test,singularity
=================================
executor >  local (16)
[c6/8a705d] process > EnvCheck (CIEcoli)                   [100%] 1 of 1 ✔
[8a/5bffcd] process > Untar (ecoli_ci_test_fast5.tar)      [100%] 1 of 1 ✔
[ba/2952e6] process > Basecall (ecoli_ci_test_fast5.tar)   [100%] 1 of 1 ✔
[50/4fc66d] process > QCExport (CIEcoli)                   [100%] 1 of 1 ✔
[cf/0eda03] process > Resquiggle (ecoli_ci_test_fast5.tar) [100%] 1 of 1 ✔
[78/1d92a2] process > Nanopolish (ecoli_ci_test_fast5.tar) [100%] 1 of 1 ✔
[15/2ab5bd] process > NplshComb (CIEcoli)                  [100%] 1 of 1 ✔
[f5/1d1786] process > DeepSignal (ecoli_ci_test_fast5.tar) [100%] 1 of 1 ✔
[d6/1eea5a] process > DpSigComb (CIEcoli)                  [100%] 1 of 1 ✔
[b8/df2702] process > Guppy (ecoli_ci_test_fast5.tar)      [100%] 1 of 1 ✔
[67/cbb8b8] process > GuppyComb (CIEcoli)                  [100%] 1 of 1 ✔
[27/cef4dc] process > Tombo (ecoli_ci_test_fast5.tar)      [100%] 1 of 1 ✔
[ca/0cc5ff] process > TomboComb (CIEcoli)                  [100%] 1 of 1 ✔
[a4/9ad71f] process > DeepMod (ecoli_ci_test_fast5.tar)    [100%] 1 of 1 ✔
[13/e907a0] process > DpmodComb (CIEcoli)                  [100%] 1 of 1 ✔
[41/edfc19] process > Report (CIEcoli)                     [100%] 1 of 1 ✔
Completed at: 29-Jan-2022 14:48:46
Duration    : 1m 26s
CPU hours   : (a few seconds)
Succeeded   : 16
But when checking the Basecall process command.log I can see :
CUDA_VISIBLE_DEVICES=
Detect no GPU, using CPU commandType
/usr/bin/guppy_basecaller
: Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 5.0.16+b9fcd7b5b

So, if I add to .bashrc export CUDA_VISIBLE_DEVICES=0 (which should not be needed), I get:
[ca/10a27b] process > EnvCheck (CIEcoli)                 [100%] 1 of 1 ✔
[a2/ff08a2] process > Untar (ecoli_ci_test_fast5.tar)    [100%] 1 of 1 ✔
[9f/bb0333] process > Basecall (ecoli_ci_test_fast5.tar) [100%] 1 of 1, failed: 1 ✔
[-        ] process > QCExport                           -
[-        ] process > Resquiggle                         -
[-        ] process > Nanopolish                         -
[-        ] process > NplshComb                          -
[-        ] process > DeepSignal                         -
[-        ] process > DpSigComb                          -
[41/ba8620] process > Guppy (ecoli_ci_test_fast5.tar)    [100%] 1 of 1, failed: 1 ✔
[-        ] process > GuppyComb                          -
[-        ] process > Tombo                              -
[-        ] process > TomboComb                          -
[-        ] process > DeepMod                            -
[-        ] process > DpmodComb                          -
[-        ] process > Report                             -
Staging foreign file: https://github.com/TheJacksonLaboratory/nanome/raw/master/test_data/ecoli_ci_test_fast5.tar.gz
Pulling Singularity image docker://liuyangzzu/nanome:v1.3 [cache /home/pedro/Documents/nanopore/211203/local_singularity_cache/liuyangzzu-nanome-v1.3.img]
Staging foreign file: https://storage.googleapis.com/jax-nanopore-01-project-data/nanome-input/model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+.tar.gz
[9f/bb0333] NOTE: Process Basecall (ecoli_ci_test_fast5.tar) terminated with an error exit status (255) -- Error is ignored
[41/ba8620] NOTE: Process Guppy (ecoli_ci_test_fast5.tar) terminated with an error exit status (255) -- Error is ignored
In the Basecall process command.log I can see:
CUDA_VISIBLE_DEVICES=0
Detect GPU, using GPU commandType
/usr/bin/guppy_basecaller
: Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 5.0.16+b9fcd7b5b
but also (CIEcoli.ecoli_ci_test_fast5.tar.Basecall.run.log):
ONT Guppy basecalling software version 5.0.16+b9fcd7b5b
config file:        /opt/ont/guppy/data/dna_r9.4.1_450bps_hac.cfg
model file:         /opt/ont/guppy/data/template_r9.4.1_450bps_hac.jsn
input path:         ecoli_ci_test_fast5.tar.untar
save path:          ecoli_ci_test_fast5.tar.basecalled
chunk size:         2000
chunks per runner:  256
minimum qscore:     9
records per file:   4000
fastq compression:  ON
num basecallers:    1
gpu device:         auto
kernel path:
runners per device: 4
[guppy/error] main: CUDA error at /builds/ofan/ont_core_cpp/ont_core/common/cuda_common.cpp:203: CUDA error at /builds/ofan/ont_core_cpp/ont_core/common/cuda_common.cpp:203: CUDA_ERROR_SYSTEM_DRIVER_MISMATCH
[guppy/warning] main: An error has occurred. Aborting.
Outside the container, I can easily resort to cuda for guppy gpu basecalling:
chunk size:         2000
chunks per runner:  512
minimum qscore:     8
records per file:   4000
fastq compression:  ON
num basecallers:    1
gpu device:         cuda:0
kernel path:
runners per device: 4
2022-01-26 15:14:54.506944 [guppy/info] crashpad_handler successfully launched.
2022-01-26 15:14:54.789242 [guppy/info] CUDA device 0 (compute 8.6) initialised, memory limit<PHONE_NUMBER>B<PHONE_NUMBER>B free)
2022-01-26 15:14:55.471325 [guppy/message] Found 428 fast5 files to process.
2022-01-26 15:14:55.485657 [guppy/message] Init time: 977 ms
2022-01-26 15:14:56.542819 [guppy/info] Read '597db6b0-2a75-4d22-8ebe-d354ec6bad3e' from file "FAQ28390_2b9848fd_0.fast5" has been loaded.

nextflow.log:
Jan-29 15:04:03.648 [main] INFO  nextflow.Nextflow - dsname              : CIEcoli
input               : https://github.com/TheJacksonLaboratory/nanome/raw/master/test_data/ecoli_ci_test_fast5.tar.gz
genome              : ecoli - [https://storage.googleapis.com/jax-nanopore-01-project-data/nanome-input/ecoli.tar.gz]
Running settings   : --------
processors          : 2
chrSet              : NC_000913.3
dataType            : ecoli
runBasecall         : Yes
runNanopolish       : Yes
runDeepSignal       : Yes
runGuppy            : Yes
runTombo            : Yes
runDeepMod          : Yes
runNANOME           : Yes
outputRaw           : true
Model summary      : --------
GUPPY_BASECALL_MODEL: dna_r9.4.1_450bps_hac.cfg
DEEPSIGNAL_MODEL_DIR/DEEPSIGNAL_MODEL: model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+/bn_17.sn_360.epoch_9.ckpt
GUPPY_METHCALL_MODEL: dna_r9.4.1_450bps_modbases_5mc_hac.cfg
DEEPMOD_RNN_MODEL   : rnn_conmodC_P100wd21_f7ne1u0_4/mod_train_conmodC_P100wd21_f3ne1u0
Pipeline settings  : --------
Working dir         : /home/pedro/Documents/nanopore/211203/work
Output dir          : results
Launch dir          : /home/pedro/Documents/nanopore/211203
Script dir          : /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome
User                : pedro
Profile             : test,singularity
Config files        : /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/nextflow.config
Pipeline Release    : master
Container           : singularity - docker://liuyangzzu/nanome:v1.3
errorStrategy       : ignore
maxRetries          : 5
Jan-29 15:04:03.649 [main] INFO  nextflow.Nextflow - =================================
Jan-29 15:04:04.006 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:EnvCheck matches process EnvCheck
Jan-29 15:04:04.011 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.011 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.015 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jan-29 15:04:04.020 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=24; memory=125.7 GB; capacity=50; pollInterval=100ms; dumpInterval=5m
Jan-29 15:04:04.041 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 25; maxThreads: 1000
Jan-29 15:04:04.094 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.094 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.100 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.101 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.124 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.124 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.134 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.134 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.146 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1]
Jan-29 15:04:04.153 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.153 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.156 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1]
Jan-29 15:04:04.163 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.163 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.172 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.172 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.176 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1, 2]
Jan-29 15:04:04.184 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.185 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.196 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.196 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.199 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1, 2]
Jan-29 15:04:04.218 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.218 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.224 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.224 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.226 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1]
Jan-29 15:04:04.233 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.234 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.239 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.239 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.241 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1]
Jan-29 15:04:04.250 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.250 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.275 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.275 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.284 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: EnvCheck, Report, METEORE, QCExport, DpSigComb, Basecall, GuppyComb, Tombo, NewTool, Untar, Resquiggle, DeepMod, NewToolComb, Nanopolish, Guppy, DpmodComb, NplshComb, TomboComb, Megalodon, DeepSignal, MgldnComb
Jan-29 15:04:04.285 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Jan-29 15:04:04.287 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Jan-29 15:04:04.288 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Jan-29 15:04:04.288 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Jan-29 15:04:04.288 [main] DEBUG nextflow.Session - Ignite dataflow network (38)
Jan-29 15:04:04.295 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > EnvCheck
Jan-29 15:04:04.296 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Untar
Jan-29 15:04:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Basecall
Jan-29 15:04:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > QCExport
Jan-29 15:04:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Resquiggle
Jan-29 15:04:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Resquiggle
Jan-29 15:04:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Nanopolish
Jan-29 15:04:04.298 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Nanopolish
Jan-29 15:04:04.298 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NplshComb
Jan-29 15:04:04.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DeepSignal
Jan-29 15:04:04.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DeepSignal
Jan-29 15:04:04.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DpSigComb
Jan-29 15:04:04.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Guppy
Jan-29 15:04:04.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Guppy
Jan-29 15:04:04.302 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GuppyComb
Jan-29 15:04:04.304 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Tombo
Jan-29 15:04:04.305 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Tombo
Jan-29 15:04:04.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TomboComb
Jan-29 15:04:04.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DeepMod
Jan-29 15:04:04.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DeepMod
Jan-29 15:04:04.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DpmodComb
Jan-29 15:04:04.307 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Report
Jan-29 15:04:04.308 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Jan-29 15:04:04.308 [main] DEBUG nextflow.Session - Session await
Jan-29 15:04:05.491 [Actor Thread 22] DEBUG n.util.BlockingThreadExecutorFactory - Thread pool name=FileTransfer; maxThreads=72; maxQueueSize=216; keepAlive=1m
Jan-29 15:04:05.496 [FileTransfer-thread-1] DEBUG nextflow.file.FilePorter - Copying foreign file https://storage.googleapis.com/jax-nanopore-01-project-data/nanome-input/ecoli.tar.gz to work dir: /home/pedro/Documents/nanopore/211203/work/stage/00/f9f02f36eeefdad0fd371c174a73c7/ecoli.tar.gz
Jan-29 15:04:05.733 [FileTransfer-thread-2] DEBUG nextflow.file.FilePorter - Copying foreign file https://storage.googleapis.com/jax-nanopore-01-project-data/nanome-input/model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+.tar.gz to work dir: /home/pedro/Documents/nanopore/211203/work/stage/17/3f93549f94c98aadaa33abe75ec1ca/model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+.tar.gz
Jan-29 15:04:05.947 [FileTransfer-thread-3] DEBUG nextflow.file.FilePorter - Copying foreign file https://github.com/TheJacksonLaboratory/nanome/raw/master/test_data/ecoli_ci_test_fast5.tar.gz to work dir: /home/pedro/Documents/nanopore/211203/work/stage/ac/7bdceb3a0dddc741c890ed4c479338/ecoli_ci_test_fast5.tar.gz
Jan-29 15:04:07.947 [Actor Thread 25] INFO  nextflow.file.FilePorter - Staging foreign file: https://github.com/TheJacksonLaboratory/nanome/raw/master/test_data/ecoli_ci_test_fast5.tar.gz
Jan-29 15:04:08.206 [Actor Thread 20] INFO  nextflow.container.SingularityCache - Pulling Singularity image docker://liuyangzzu/nanome:v1.3 [cache /home/pedro/Documents/nanopore/211203/local_singularity_cache/liuyangzzu-nanome-v1.3.img]
Jan-29 15:04:08.891 [Actor Thread 22] INFO  nextflow.file.FilePorter - Staging foreign file: https://storage.googleapis.com/jax-nanopore-01-project-data/nanome-input/model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+.tar.gz
Jan-29 15:04:12.191 [Actor Thread 20] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=docker://liuyangzzu/nanome:v1.3 path=/home/pedro/Documents/nanopore/211203/local_singularity_cache/liuyangzzu-nanome-v1.3.img
Jan-29 15:04:12.282 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 15:04:12.286 [Task submitter] INFO  nextflow.Session - [a2/ff08a2] Submitted process > Untar (ecoli_ci_test_fast5.tar)
Jan-29 15:04:12.790 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: Untar (ecoli_ci_test_fast5.tar); status: COMPLETED; exit: 0; error: -; workDir: /home/pedro/Documents/nanopore/211203/work/a2/ff08a2905c3972cc682b51622b44ed]
Jan-29 15:04:12.842 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 15:04:12.843 [Task submitter] INFO  nextflow.Session - [9f/bb0333] Submitted process > Basecall (ecoli_ci_test_fast5.tar)
Jan-29 15:04:14.226 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: Basecall (ecoli_ci_test_fast5.tar); status: COMPLETED; exit: 255; error: -; workDir: /home/pedro/Documents/nanopore/211203/work/9f/bb0333f896fb508bd348bc98bc830e]
Jan-29 15:04:14.234 [Task monitor] INFO  nextflow.processor.TaskProcessor - [9f/bb0333] NOTE: Process Basecall (ecoli_ci_test_fast5.tar) terminated with an error exit status (255) -- Error is ignored
Jan-29 15:04:28.441 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/null1
Jan-29 15:04:28.444 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/validate_nanome_container.sh
Jan-29 15:04:28.444 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/gcf52ref.patch
Jan-29 15:04:28.444 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/sum_chr_mod.py
Jan-29 15:04:28.444 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/clean_old_basecall_in_fast5.py
Jan-29 15:04:28.444 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/combination_model_prediction.py
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/unify_format_for_calls.sh
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/null3
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/preindexing_check_dups.py
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/hm_cluster_predict.py
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/gcf52ref.tar.gz
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/null2
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/extract_methylation_fast5_support_dir.py
Jan-29 15:04:28.446 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/tombo_extract_per_read_stats.py
Jan-29 15:04:28.446 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/FilesSeparator.sh
Jan-29 15:04:28.446 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/FilesSeparator.py
Jan-29 15:04:28.454 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 15:04:28.455 [Task submitter] INFO  nextflow.Session - [ca/10a27b] Submitted process > EnvCheck (CIEcoli)
Jan-29 15:04:38.309 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: EnvCheck (CIEcoli); status: COMPLETED; exit: 0; error: -; workDir: /home/pedro/Documents/nanopore/211203/work/ca/10a27b848b85590e50e99c47fc4839]
Jan-29 15:04:38.310 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process EnvCheck (CIEcoli) is unable to find [UnixPath]: /home/pedro/Documents/nanopore/211203/work/ca/10a27b848b85590e50e99c47fc4839/rerio (pattern: rerio)
Jan-29 15:04:38.378 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process EnvCheck > Skipping output binding because one or more optional files are missing: fileoutparam<1>
Jan-29 15:04:38.453 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 15:04:38.454 [Task submitter] INFO  nextflow.Session - [41/ba8620] Submitted process > Guppy (ecoli_ci_test_fast5.tar)
Jan-29 15:04:39.813 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: Guppy (ecoli_ci_test_fast5.tar); status: COMPLETED; exit: 255; error: -; workDir: /home/pedro/Documents/nanopore/211203/work/41/ba862049350f4d29c6d65fed9a4830]
Jan-29 15:04:39.814 [Task monitor] INFO  nextflow.processor.TaskProcessor - [41/ba8620] NOTE: Process Guppy (ecoli_ci_test_fast5.tar) terminated with an error exit status (255) -- Error is ignored
Jan-29 15:04:39.817 [main] DEBUG nextflow.Session - Session await > all process finished
Jan-29 15:04:39.913 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jan-29 15:04:39.923 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=2; failedCount=2; ignoredCount=2; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=10.2s; failedDuration=2.6s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=0; ]
Jan-29 15:04:39.949 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
Jan-29 15:04:39.963 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

Hi,
The error message CUDA_ERROR_SYSTEM_DRIVER_MISMATCH  means the docker/singularity container's cuda driver is not compatible with your GPU devices.  We have tested may GPU devices without problems: such as nvidia-tesla-p100, nvidia-tesla-v100, etc.
Can you go to the failed Basecall process [9f/bb0333] process > Basecall (ecoli_ci_test_fast5.tar) [100%] 1 of 1, failed: 1 ✔
cd work/9f/bb0333

Then, test if your local running guppy basecaller script can be ok?
Compare two ways of runing:

Below will be a local running of the script, using your local system's cuda driver

bash -x .command.sh

Below is the docker's calling of the script, using our default container's cuda driver

docker run -v $PWD:$PWD -w $PWD  liuyangzzu/nanome:v1.3   bash -x .command.sh

If you can run in your local runing, but failed with our container with error message CUDA_ERROR_SYSTEM_DRIVER_MISMATCH. I suggest to chose one of below two ways to run NANOME:

local running, check doc here: https://github.com/TheJacksonLaboratory/nanome/blob/master/docs/Usage.md#6-conda-environment-for-local-running
build your container by installing your GPU specific driver, based on NANOME GitHub's Dockerfile: https://github.com/TheJacksonLaboratory/nanome/blob/master/Dockerfile

Since your GPU specific cuda driver can work ok in your workstation, you can directly use local running NANOME:

Create the conda env

git clone https://github.com/TheJacksonLaboratory/nanome.git
cd nanome
conda env create --name nanome --file=environment.yml
conda activate nanome

pip install megalodon==2.4.1
npm install -g inliner
conda install -c conda-forge -c bioconda nextflow

Run pipeline:

# Run NANOME pipeline using local execution
conda activate nanome
nextflow run TheJacksonLaboratory/nanome\
    -profile test\
    --guppyDir [guppy-installation-directory]

nextflow.log:
Jan-29 15:04:03.648 [main] INFO  nextflow.Nextflow - dsname              : CIEcoli
input               : https://github.com/TheJacksonLaboratory/nanome/raw/master/test_data/ecoli_ci_test_fast5.tar.gz
genome              : ecoli - [https://storage.googleapis.com/jax-nanopore-01-project-data/nanome-input/ecoli.tar.gz]
Running settings   : --------
processors          : 2
chrSet              : NC_000913.3
dataType            : ecoli
runBasecall         : Yes
runNanopolish       : Yes
runDeepSignal       : Yes
runGuppy            : Yes
runTombo            : Yes
runDeepMod          : Yes
runNANOME           : Yes
outputRaw           : true
Model summary      : --------
GUPPY_BASECALL_MODEL: dna_r9.4.1_450bps_hac.cfg
DEEPSIGNAL_MODEL_DIR/DEEPSIGNAL_MODEL: model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+/bn_17.sn_360.epoch_9.ckpt
GUPPY_METHCALL_MODEL: dna_r9.4.1_450bps_modbases_5mc_hac.cfg
DEEPMOD_RNN_MODEL   : rnn_conmodC_P100wd21_f7ne1u0_4/mod_train_conmodC_P100wd21_f3ne1u0
Pipeline settings  : --------
Working dir         : /home/pedro/Documents/nanopore/211203/work
Output dir          : results
Launch dir          : /home/pedro/Documents/nanopore/211203
Script dir          : /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome
User                : pedro
Profile             : test,singularity
Config files        : /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/nextflow.config
Pipeline Release    : master
Container           : singularity - docker://liuyangzzu/nanome:v1.3
errorStrategy       : ignore
maxRetries          : 5
Jan-29 15:04:03.649 [main] INFO  nextflow.Nextflow - =================================
Jan-29 15:04:04.006 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:EnvCheck matches process EnvCheck
Jan-29 15:04:04.011 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.011 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.015 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jan-29 15:04:04.020 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=24; memory=125.7 GB; capacity=50; pollInterval=100ms; dumpInterval=5m
Jan-29 15:04:04.041 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 25; maxThreads: 1000
Jan-29 15:04:04.094 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.094 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.100 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.101 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.124 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.124 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.134 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.134 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.146 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1]
Jan-29 15:04:04.153 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.153 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.156 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1]
Jan-29 15:04:04.163 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.163 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.172 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.172 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.176 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1, 2]
Jan-29 15:04:04.184 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.185 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.196 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.196 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.199 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1, 2]
Jan-29 15:04:04.218 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.218 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.224 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.224 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.226 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1]
Jan-29 15:04:04.233 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.234 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.239 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.239 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.241 [main] DEBUG nextflow.processor.TaskProcessor - Creating combiner operator for each param(s) at index(es): [1]
Jan-29 15:04:04.250 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.250 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.275 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-29 15:04:04.275 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-29 15:04:04.284 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: EnvCheck, Report, METEORE, QCExport, DpSigComb, Basecall, GuppyComb, Tombo, NewTool, Untar, Resquiggle, DeepMod, NewToolComb, Nanopolish, Guppy, DpmodComb, NplshComb, TomboComb, Megalodon, DeepSignal, MgldnComb
Jan-29 15:04:04.285 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Jan-29 15:04:04.287 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Jan-29 15:04:04.288 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Jan-29 15:04:04.288 [main] DEBUG nextflow.extension.CH - Bridging dataflow queue=DataflowQueue(queue=[])
Jan-29 15:04:04.288 [main] DEBUG nextflow.Session - Ignite dataflow network (38)
Jan-29 15:04:04.295 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > EnvCheck
Jan-29 15:04:04.296 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Untar
Jan-29 15:04:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Basecall
Jan-29 15:04:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > QCExport
Jan-29 15:04:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Resquiggle
Jan-29 15:04:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Resquiggle
Jan-29 15:04:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Nanopolish
Jan-29 15:04:04.298 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Nanopolish
Jan-29 15:04:04.298 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NplshComb
Jan-29 15:04:04.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DeepSignal
Jan-29 15:04:04.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DeepSignal
Jan-29 15:04:04.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DpSigComb
Jan-29 15:04:04.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Guppy
Jan-29 15:04:04.299 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Guppy
Jan-29 15:04:04.302 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > GuppyComb
Jan-29 15:04:04.304 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Tombo
Jan-29 15:04:04.305 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Tombo
Jan-29 15:04:04.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > TomboComb
Jan-29 15:04:04.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DeepMod
Jan-29 15:04:04.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DeepMod
Jan-29 15:04:04.306 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > DpmodComb
Jan-29 15:04:04.307 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > Report
Jan-29 15:04:04.308 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Jan-29 15:04:04.308 [main] DEBUG nextflow.Session - Session await
Jan-29 15:04:05.491 [Actor Thread 22] DEBUG n.util.BlockingThreadExecutorFactory - Thread pool name=FileTransfer; maxThreads=72; maxQueueSize=216; keepAlive=1m
Jan-29 15:04:05.496 [FileTransfer-thread-1] DEBUG nextflow.file.FilePorter - Copying foreign file https://storage.googleapis.com/jax-nanopore-01-project-data/nanome-input/ecoli.tar.gz to work dir: /home/pedro/Documents/nanopore/211203/work/stage/00/f9f02f36eeefdad0fd371c174a73c7/ecoli.tar.gz
Jan-29 15:04:05.733 [FileTransfer-thread-2] DEBUG nextflow.file.FilePorter - Copying foreign file https://storage.googleapis.com/jax-nanopore-01-project-data/nanome-input/model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+.tar.gz to work dir: /home/pedro/Documents/nanopore/211203/work/stage/17/3f93549f94c98aadaa33abe75ec1ca/model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+.tar.gz
Jan-29 15:04:05.947 [FileTransfer-thread-3] DEBUG nextflow.file.FilePorter - Copying foreign file https://github.com/TheJacksonLaboratory/nanome/raw/master/test_data/ecoli_ci_test_fast5.tar.gz to work dir: /home/pedro/Documents/nanopore/211203/work/stage/ac/7bdceb3a0dddc741c890ed4c479338/ecoli_ci_test_fast5.tar.gz
Jan-29 15:04:07.947 [Actor Thread 25] INFO  nextflow.file.FilePorter - Staging foreign file: https://github.com/TheJacksonLaboratory/nanome/raw/master/test_data/ecoli_ci_test_fast5.tar.gz
Jan-29 15:04:08.206 [Actor Thread 20] INFO  nextflow.container.SingularityCache - Pulling Singularity image docker://liuyangzzu/nanome:v1.3 [cache /home/pedro/Documents/nanopore/211203/local_singularity_cache/liuyangzzu-nanome-v1.3.img]
Jan-29 15:04:08.891 [Actor Thread 22] INFO  nextflow.file.FilePorter - Staging foreign file: https://storage.googleapis.com/jax-nanopore-01-project-data/nanome-input/model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+.tar.gz
Jan-29 15:04:12.191 [Actor Thread 20] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=docker://liuyangzzu/nanome:v1.3 path=/home/pedro/Documents/nanopore/211203/local_singularity_cache/liuyangzzu-nanome-v1.3.img
Jan-29 15:04:12.282 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 15:04:12.286 [Task submitter] INFO  nextflow.Session - [a2/ff08a2] Submitted process > Untar (ecoli_ci_test_fast5.tar)
Jan-29 15:04:12.790 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: Untar (ecoli_ci_test_fast5.tar); status: COMPLETED; exit: 0; error: -; workDir: /home/pedro/Documents/nanopore/211203/work/a2/ff08a2905c3972cc682b51622b44ed]
Jan-29 15:04:12.842 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 15:04:12.843 [Task submitter] INFO  nextflow.Session - [9f/bb0333] Submitted process > Basecall (ecoli_ci_test_fast5.tar)
Jan-29 15:04:14.226 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: Basecall (ecoli_ci_test_fast5.tar); status: COMPLETED; exit: 255; error: -; workDir: /home/pedro/Documents/nanopore/211203/work/9f/bb0333f896fb508bd348bc98bc830e]
Jan-29 15:04:14.234 [Task monitor] INFO  nextflow.processor.TaskProcessor - [9f/bb0333] NOTE: Process Basecall (ecoli_ci_test_fast5.tar) terminated with an error exit status (255) -- Error is ignored
Jan-29 15:04:28.441 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/null1
Jan-29 15:04:28.444 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/validate_nanome_container.sh
Jan-29 15:04:28.444 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/gcf52ref.patch
Jan-29 15:04:28.444 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/sum_chr_mod.py
Jan-29 15:04:28.444 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/clean_old_basecall_in_fast5.py
Jan-29 15:04:28.444 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/combination_model_prediction.py
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/unify_format_for_calls.sh
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/null3
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/preindexing_check_dups.py
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/hm_cluster_predict.py
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/gcf52ref.tar.gz
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/null2
Jan-29 15:04:28.445 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/extract_methylation_fast5_support_dir.py
Jan-29 15:04:28.446 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/tombo_extract_per_read_stats.py
Jan-29 15:04:28.446 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/FilesSeparator.sh
Jan-29 15:04:28.446 [Actor Thread 22] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/pedro/.nextflow/assets/TheJacksonLaboratory/nanome/utils/FilesSeparator.py
Jan-29 15:04:28.454 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 15:04:28.455 [Task submitter] INFO  nextflow.Session - [ca/10a27b] Submitted process > EnvCheck (CIEcoli)
Jan-29 15:04:38.309 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: EnvCheck (CIEcoli); status: COMPLETED; exit: 0; error: -; workDir: /home/pedro/Documents/nanopore/211203/work/ca/10a27b848b85590e50e99c47fc4839]
Jan-29 15:04:38.310 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process EnvCheck (CIEcoli) is unable to find [UnixPath]: /home/pedro/Documents/nanopore/211203/work/ca/10a27b848b85590e50e99c47fc4839/rerio (pattern: rerio)
Jan-29 15:04:38.378 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process EnvCheck > Skipping output binding because one or more optional files are missing: fileoutparam<1>
Jan-29 15:04:38.453 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-29 15:04:38.454 [Task submitter] INFO  nextflow.Session - [41/ba8620] Submitted process > Guppy (ecoli_ci_test_fast5.tar)
Jan-29 15:04:39.813 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: Guppy (ecoli_ci_test_fast5.tar); status: COMPLETED; exit: 255; error: -; workDir: /home/pedro/Documents/nanopore/211203/work/41/ba862049350f4d29c6d65fed9a4830]
Jan-29 15:04:39.814 [Task monitor] INFO  nextflow.processor.TaskProcessor - [41/ba8620] NOTE: Process Guppy (ecoli_ci_test_fast5.tar) terminated with an error exit status (255) -- Error is ignored
Jan-29 15:04:39.817 [main] DEBUG nextflow.Session - Session await > all process finished
Jan-29 15:04:39.913 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jan-29 15:04:39.923 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=2; failedCount=2; ignoredCount=2; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=10.2s; failedDuration=2.6s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=0; ]
Jan-29 15:04:39.949 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
Jan-29 15:04:39.963 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye


Bug: Display nothing in "Read Caption from Select Image"

As title.
Since the version 0.2.0, "Caption of Selected Image" is empty whether I have tags or not. The problem is solved when I change to version "0.1.2" and there's no log in the terminal window

Same issue here. Will also try to reset to 0.1.2.

Yes, you have to check out tag yourself.

I ended up rolling back to b8730ad53b64f41c56d23e859ffc66e91d8aad91.

I ended up rolling back to b8730ad.

i tried this and now its not infinitely loading, but still gives an error saying All files must contained within the Gradio python app working directory, or be a temp file created by the Gradio python app.


Change version number from 2.4 to 2.3 - NuGet Test Utilities package

Overview
Changes version number from 2.4 to 2.3 for the NuGet Test Utilities PR: #7032
Changes

Updates version number

Verification

As a reviewer, it is possible to check out this change locally by using the following
commands (substituting {PR_ID} with the ID of this pull request):
git fetch origin pull/{PR_ID}/head:name_of_local_branch
git checkout name_of_local_branch

/azp run

/azp run