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[Bug]: test run fails (again) #18

Closed ChristopherRichie closed 1 year ago

ChristopherRichie commented 1 year ago

What happened?

I am running on the NIH HPC, with nextflow singularity CUDA When I run the test command, i get this error:

 nextflow run epi2me-labs/wf-clone-validation         --fastq test_data/test         --db_directory wf-clone-validation-db         --threads 4
N E X T F L O W  ~  version 22.10.4
Launching `https://github.com/epi2me-labs/wf-clone-validation` [infallible_venter] DSL2 - revision: 8f800c1aa5 [master]

WARN: Found unexpected parameters:
* --igenomes_base: /fdb/igenomes/
* --max_time: 72 h
* --max_cpus: 32
* --max_memory: 224 GB
* --config_profile_url: https://hpc.nih.gov/apps/nextflow.html
* --config_profile_contact: staff@hpc.nih.gov
* --config_profile_description: Biowulf nf-core config
- Ignore this warning: params.schema_ignore_params = "igenomes_base,max_time,max_cpus,max_memory,config_profile_url,config_profile_contact,config_profile_description"

||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-clone-validation v0.2.12-g8f800c1
--------------------------------------------------------------------------------
Core Nextflow options
  revision       : master
  runName        : infallible_venter
  containerEngine: docker
  launchDir      : /gpfs/gsfs12/users/chrisr/CR3271/no_sample/20230327_2016_MC-110461_amx905_e1685120
  workDir        : /gpfs/gsfs12/users/chrisr/CR3271/no_sample/20230327_2016_MC-110461_amx905_e1685120/work
  projectDir     : /home/chrisr/.nextflow/22.10.2/assets/epi2me-labs/wf-clone-validation
  userName       : chrisr
  profile        : standard
  configFiles    : /home/chrisr/.nextflow/22.10.2/assets/epi2me-labs/wf-clone-validation/nextflow.config, /gpfs/gsfs12/users/chrisr/CR3271/no_sample/20230327_2016_MC-110461_amx905_e1685120/nextflow.config

Input Options
  fastq          : test_data/test
  primers        : /home/chrisr/.nextflow/22.10.2/assets/epi2me-labs/wf-clone-validation/data/primers.tsv

Reference Genome Options
  db_directory   : wf-clone-validation-db

Sample Options
  min_barcode    : 0
  max_barcode    : 192

!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-clone-validation for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

--------------------------------------------------------------------------------
This is epi2me-labs/wf-clone-validation v0.2.12-g8f800c1.
--------------------------------------------------------------------------------
Checking fastq input.
executor >  local (3)
[ad/8db171] process > fastcat (3)                   [  0%] 0 of 2
[-        ] process > pipeline:checkIfEnoughReads   -
executor >  local (4)
[ad/8db171] process > fastcat (3)                      [ 33%] 1 of 3, failed: 1
[-        ] process > pipeline:checkIfEnoughReads      -
[-        ] process > pipeline:assembleCore            -
[88/08665c] process > pipeline:lookup_medaka_model (1) [  0%] 0 of 1
[-        ] process > pipeline:medakaPolishAssembly    -
[-        ] process > pipeline:downsampledStats        -
[-        ] process > pipeline:findPrimers             -
[cb/7109f0] process > pipeline:medakaVersion           [100%] 1 of 1, failed: 1 ✘
[-        ] process > pipeline:getVersions             -
[c0/c8b867] process > pipeline:getParams               [100%] 1 of 1, failed: 1 ✘
[-        ] process > pipeline:runPlannotate           -
[-        ] process > pipeline:inserts                 -
[-        ] process > pipeline:report                  -
[-        ] process > output                           -
Error executing process > 'fastcat (3)'

Caused by:
  Process `fastcat (3)` terminated with an error exit status (127)

Command executed:

  mkdir fastcat_stats
  fastcat             -s barcode03             -r fastcat_stats/per-read-stats.tsv             -f fastcat_stats/per-file-stats.tsv             -a 3500 -b 10500             barcode03             | bgzip -@ 4 > seqs.fastq.gz

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.run: line 281: docker: command not found

Work dir:
  /gpfs/gsfs12/users/chrisr/CR3271/no_sample/20230327_2016_MC-110461_amx905_e1685120/work/ad/8db1714d5b338b0b8f5a34d0e38a75

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

WARN: Killing running tasks (1)

[chrisr@cn4466 20230327_2016_MC-110461_amx905_e1685120]$

Operating System

Windows 10

Workflow Execution

EPI2ME Labs desktop application

Workflow Execution - EPI2ME Labs Versions

No response

Workflow Execution - CLI Execution Profile

None

Workflow Version

N E X T F L O W ~ version 22.10.4 Launching https://github.com/epi2me-labs/wf-clone-validation [infallible_venter] DSL2 - revision: 8f800c1aa5 [master]

Relevant log output

nextflow run epi2me-labs/wf-clone-validation         --fastq test_data/test         --db_directory wf-clone-validation-db         --threads 4
N E X T F L O W  ~  version 22.10.4
Launching `https://github.com/epi2me-labs/wf-clone-validation` [infallible_venter] DSL2 - revision: 8f800c1aa5 [master]

WARN: Found unexpected parameters:
* --igenomes_base: /fdb/igenomes/
* --max_time: 72 h
* --max_cpus: 32
* --max_memory: 224 GB
* --config_profile_url: https://hpc.nih.gov/apps/nextflow.html
* --config_profile_contact: staff@hpc.nih.gov
* --config_profile_description: Biowulf nf-core config
- Ignore this warning: params.schema_ignore_params = "igenomes_base,max_time,max_cpus,max_memory,config_profile_url,config_profile_contact,config_profile_description"

||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-clone-validation v0.2.12-g8f800c1
--------------------------------------------------------------------------------
Core Nextflow options
  revision       : master
  runName        : infallible_venter
  containerEngine: docker
  launchDir      : /gpfs/gsfs12/users/chrisr/CR3271/no_sample/20230327_2016_MC-110461_amx905_e1685120
  workDir        : /gpfs/gsfs12/users/chrisr/CR3271/no_sample/20230327_2016_MC-110461_amx905_e1685120/work
  projectDir     : /home/chrisr/.nextflow/22.10.2/assets/epi2me-labs/wf-clone-validation
  userName       : chrisr
  profile        : standard
  configFiles    : /home/chrisr/.nextflow/22.10.2/assets/epi2me-labs/wf-clone-validation/nextflow.config, /gpfs/gsfs12/users/chrisr/CR3271/no_sample/20230327_2016_MC-110461_amx905_e1685120/nextflow.config

Input Options
  fastq          : test_data/test
  primers        : /home/chrisr/.nextflow/22.10.2/assets/epi2me-labs/wf-clone-validation/data/primers.tsv

Reference Genome Options
  db_directory   : wf-clone-validation-db

Sample Options
  min_barcode    : 0
  max_barcode    : 192

!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-clone-validation for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

--------------------------------------------------------------------------------
This is epi2me-labs/wf-clone-validation v0.2.12-g8f800c1.
--------------------------------------------------------------------------------
Checking fastq input.
executor >  local (3)
[ad/8db171] process > fastcat (3)                   [  0%] 0 of 2
[-        ] process > pipeline:checkIfEnoughReads   -
executor >  local (4)
[ad/8db171] process > fastcat (3)                      [ 33%] 1 of 3, failed: 1
[-        ] process > pipeline:checkIfEnoughReads      -
[-        ] process > pipeline:assembleCore            -
[88/08665c] process > pipeline:lookup_medaka_model (1) [  0%] 0 of 1
[-        ] process > pipeline:medakaPolishAssembly    -
[-        ] process > pipeline:downsampledStats        -
[-        ] process > pipeline:findPrimers             -
[cb/7109f0] process > pipeline:medakaVersion           [100%] 1 of 1, failed: 1 ✘
[-        ] process > pipeline:getVersions             -
[c0/c8b867] process > pipeline:getParams               [100%] 1 of 1, failed: 1 ✘
[-        ] process > pipeline:runPlannotate           -
[-        ] process > pipeline:inserts                 -
[-        ] process > pipeline:report                  -
[-        ] process > output                           -
Error executing process > 'fastcat (3)'

Caused by:
  Process `fastcat (3)` terminated with an error exit status (127)

Command executed:

  mkdir fastcat_stats
  fastcat             -s barcode03             -r fastcat_stats/per-read-stats.tsv             -f fastcat_stats/per-file-stats.tsv             -a 3500 -b 10500             barcode03             | bgzip -@ 4 > seqs.fastq.gz

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.run: line 281: docker: command not found

Work dir:
  /gpfs/gsfs12/users/chrisr/CR3271/no_sample/20230327_2016_MC-110461_amx905_e1685120/work/ad/8db1714d5b338b0b8f5a34d0e38a75

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

WARN: Killing running tasks (1)

[chrisr@cn4466 20230327_2016_MC-110461_amx905_e1685120]$

I am running on the NIH HPC, 
[chrisr@cn4466 20230327_2016_MC-110461_amx905_e1685120]$ cat /etc/os-release
NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:7"
HOME_URL="https://www.centos.org/"
BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7"
CENTOS_MANTISBT_PROJECT_VERSION="7"
REDHAT_SUPPORT_PRODUCT="centos"
REDHAT_SUPPORT_PRODUCT_VERSION="7"
cjw85 commented 1 year ago

Hi @ChristopherRichie,

Looking at your logs it seems to me that you are automatically loading additional Nextflow config files (presumably in you home directory?).

The error here is that you don't have docker available on your cluster, which is assumed by our default Nextflow profile. You will need to provide the name of your institution specific Nextflow profile (judging by some of the other logging it looks like your additional config is an nf-core institutional profile).

All the workflow code is available as container images on Dockerhub that should be useable from your HPCs preferred tool for running containers.

ChristopherRichie commented 1 year ago

Hi Chris, thanks for the fast reply.

The README indicates that either Docker or Singularity is sufficient to run the workflow.

NIH BIOWULF HPC will only allow Singularity. (Docker is not available.)

Can you clarify if this workflow will work with singularity alone?

If so, can you suggest how I might modify my nextflow.config (s) to work without Docker?

Thanks

From: Chris Wright @.> Sent: Wednesday, April 19, 2023 12:59 PM To: epi2me-labs/wf-clone-validation @*.**@*.> Cc: Richie, Christopher (NIH/NIDA) [E] @.>; Mention @.***> Subject: [EXTERNAL] Re: [epi2me-labs/wf-clone-validation] [Bug]: test run fails (again) (Issue #18)

Hi @ChristopherRichiehttps://github.com/ChristopherRichie,

Looking at your logs it seems to me that you are automatically loading additional Nextflow config files (presumably in you home directory?).

The error here is that you don't have docker available on your cluster, which is assumed by our default Nextflow profile. You will need to provide the name of your institution specific Nextflow profile (judging by some of the other logging it looks like your additional config is an nf-core institutional profile).

All the workflow code is available as container images on Dockerhub that should be useable from your HPCs preferred tool for running containers.

- Reply to this email directly, view it on GitHubhttps://github.com/epi2me-labs/wf-clone-validation/issues/18#issuecomment-1515069984, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AR4COQ47XBPCKBTDFTXG2QDXCAKTTANCNFSM6AAAAAAXEKZI2U. You are receiving this because you were mentioned.Message ID: @.**@.>> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

cjw85 commented 1 year ago

The workflow can run with singularity. How to do that depends intimately on your cluster setup. You should talk to your cluster administrators for advice.

Following the breadcrumbs from your log messages led me to https://hpc.nih.gov/apps/nextflow.html which appears to contains useful information. Your institutional nextflow config appears to provide a biowolf profile that you likely need to set. Though I can't really comment and again you should talk to your cluster admins.

ChristopherRichie commented 1 year ago

Thanks Chris

thanks for confirming that the wf can work with just singularity. I will follow up with my cluster admins

Thanks

From: Chris Wright @.> Sent: Wednesday, April 19, 2023 4:08 PM To: epi2me-labs/wf-clone-validation @.> Cc: Richie, Christopher (NIH/NIDA) [E] @.>; Mention @.> Subject: [EXTERNAL] Re: [epi2me-labs/wf-clone-validation] [Bug]: test run fails (again) (Issue #18)

The workflow can run with singularity. How to do that depends intimately on your cluster setup. You should talk to your cluster administrators for advice.

Following the breadcrumbs from your log messages led me to https://hpc.nih.gov/apps/nextflow.html which appears to contains useful information. Your institutional nextflow config appears to provide a biowolf profile that you likely need to set. Though I can't really comment and again you should talk to your cluster admins.

- Reply to this email directly, view it on GitHubhttps://github.com/epi2me-labs/wf-clone-validation/issues/18#issuecomment-1515313486, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AR4COQ6U4EQPQQ2ISNSD543XCBAZTANCNFSM6AAAAAAXEKZI2U. You are receiving this because you were mentioned.Message ID: @.**@.>> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

sarahjeeeze commented 1 year ago

Closing through lack of response from original poster