'Test it on a minimal dataset by running' does not work

Hi again.

Today, I installed metaGT on our machine using git clone.

After installing it, I tried to test the minimal dataset described in README - 'Quick Start' - 4, but it did not work.

(metaGT) pclee@bio507-3:/analysis/users/wycho/Project/metaGT$ nextflow run metaGT -profile test,conda
N E X T F L O W  ~  version 22.10.6
Launching `metaGT/main.nf` [distraught_bardeen] DSL2 - revision: 53a1fce0fe


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  metaGT v1.0dev
------------------------------------------------------


WARN: Found unexpected parameters:
* --single_end: false
- Ignore this warning: params.schema_ignore_params = "single_end"

Core Nextflow options
  runName                   : distraught_bardeen
  container                 : metaGT:dev
  launchDir                 : /analysis/users/wycho/Project/metaGT
  workDir                   : /analysis/users/wycho/Project/metaGT/work
  projectDir                : /analysis/users/wycho/Project/metaGT/metaGT
  userName                  : pclee
  profile                   : test,conda
  configFiles               : /analysis/users/wycho/Project/metaGT/metaGT/nextflow.config

Input/output options
  dna_reads                 : null
  rna_reads                 : null

Pipeline options
  transcriptome             : /analysis/users/wycho/Project/metaGT/metaGT/data/transcriptome.fasta
  genome                    : /analysis/users/wycho/Project/metaGT/metaGT/data/genome.fasta

Generic options
  enable_conda              : true

Max job request options
  max_cpus                  : 2
  max_memory                : 6 GB
  max_time                  : 2d

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

------------------------------------------------------
 Only displaying parameters that differ from defaults.
------------------------------------------------------
executor >  local (2)
[e0/189a38] process > MINIMAP2 (genome) [  0%] 0 of 1
executor >  local (2)
[e0/189a38] process > MINIMAP2 (genome) [100%] 1 of 1, failed: 1 ✘
[93/35c80a] process > PROKKA (genome)   [100%] 1 of 1, failed: 1 ✘
executor >  local (2)
[e0/189a38] process > MINIMAP2 (genome) [100%] 1 of 1, failed: 1 ✘
[93/35c80a] process > PROKKA (genome)   [100%] 1 of 1, failed: 1 ✘
[-        ] process > COVERED_CDS       -
[-        ] process > TRANSDECODER      -
[-        ] process > MMSEQS_CLUSTER    -
Execution cancelled -- Finishing pending tasks before exit
- Ignore this warning: params.schema_ignore_params = "single_end"
WARN: Found unexpected parameters:
* --single_end: false
WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info.
Error executing process > 'MINIMAP2 (genome)'

Caused by:
  Process `MINIMAP2 (genome)` terminated with an error exit status (127)

Command executed:

  minimap2 -t 2 -aY --MD genome.fasta transcriptome.fasta > genome.align.sam

  samtools sort genome.align.sam -o genome.align.sorted.bam

  change_name.py  transcriptome.fasta transcriptome.all_transcripts.fasta

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 2: minimap2: command not found

Work dir:
  /analysis/users/wycho/Project/metaGT/work/e0/189a3802f3a24a22cbc95071249249

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`


Unknown method invocation `checkHostname`

 -- Check script 'metaGT/main.nf' at line: 270 or see '.nextflow.log' file for more details

Is this caused by my incorrect command? Then, how can I solve it?

Best,
Lafmas

@andrewprzh

Hi again

WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info.

this issue was solved when I installed graphviz using conda install -c bioconda perl-graphviz

but

WARN: Found unexpected parameters: * --single_end: false

this is issue still remain

@andrewprzh Should I ask you how to solve it?

Best,
Lafmas

@Lafmas

Dear @Lafmas

I haven't seen the graphvis warning before. The one about single-end can be ignored, it should not affect the run.

Conda is installed, correct?

Best
Andrey

@andrewprzh

Dear @andrewprzh

Thank you for your reply.

Warning for graphviz already solved.

How can I ignore the warning about single-end? Insert nextflow run metaGT -profile test --params.schema_ignore_params = "single_end" command only displayed Unexpected error [StackOverflowError].

I installed nextflow and metaGT using conda environment.

Best,
Lafmas

@Lafmas

Dear @Lafmas

As far as I understand this warning does not affect the run, right? It sill completes despite the warning?

Best
Andrey

I update the code, the warning should not appear anymore.

Best
Andrey

@andrewprzh

Dear @andrewprzh

Thank you! I will try a test analysis.

Best,
Lafmas

@andrewprzh

Dear @andrewprzh

Unfortunately, the error we previously discussed still exists.

I have attached a screenshot of my terminal to give you a clearer picture. It seems minimap2 and prokka still do not working properly.

Thank you for your consistent help and support.

Best,
Lafmas

(metaGT) pclee@bio507-3:/analysis/users/wycho/Project$ nextflow run metaGT -profile test,conda
N E X T F L O W ~ version 22.10.6
Launching metaGT/main.nf [festering_curran] DSL2 - revision: 53a1fce0fe

@Lafmas

Dear @Lafmas

At some point something changed in Nextflow and automatic conda installation broke.
Shouldbe fixed now, could you update and try again?

Best
Andrey

@andrewprzh

Dear @andrewprzh

Sure. I will try it.

As soon as the results are confirmed, I will share them here

Best
Lafmas

@andrewprzh

Dear @andrewprzh

I deleted the existing conda environment and installed Nextflow & metaGT newly again.

Afterward, I am running the test file and this time the process seems to be working well!

The analysis is currently underway and I will share the results here once it's complete.

Best
Lafmas

@andrewprzh

Dear @andrewprzh

Unfortunately, the process was stopped.

I have attached screenshot of the error. And I'll see if there are any problems with my conda environment.

Best
Lafmas

@Lafmas

Dear @Lafmas

Looks like a conda problem - the environment was not created and it does not even tell what the error is.
Could you try running the same command manually:
conda create -n metagt --file metaGT/environment.yml
?

Best
Andrey

@andrewprzh

Dear @andrewprzh

I write because I have the same problem, it has not been possible to create the environment, it generates the same error seen in the thread, it seems that conda is able to install minimap2. Even trying to create the environment directly with the conda command, it never finishes creating. What I find strange is that with the command "conda install -c bioconda minimap2" it is able to install minimap2.

here is a part of the problem shown in the nextflow.log file

"Aug-14 00:37:39.031 [Task monitor] DEBUG n.processor.TaskPollingMonitor - No more task to compute -- The following nodes are still active:
[process] MINIMAP2
status=ACTIVE
port 0: (queue) closed; channel: -
port 1: (queue) OPEN ; channel: -
port 2: (cntrl) - ; channel: $

[process] COVERED_CDS
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (queue) OPEN ; channel: -
port 2: (queue) OPEN ; channel: -
port 3: (queue) OPEN ; channel: -
port 4: (cntrl) - ; channel: $

[process] TRANSDECODER
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $

[process] MMSEQS_CLUSTER
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (queue) OPEN ; channel: -
port 2: (cntrl) - ; channel: $

Aug-14 00:37:39.272 [Actor Thread 9] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=MINIMAP2 (1); work-dir=null
error [java.lang.IllegalStateException]: java.lang.IllegalStateException: Failed to create Conda environment
command: conda env create --prefix /home/call/MetaGT/work/conda/metaGT-1.0-f7c8dc3121d55495d60aeb53bd2259e3 --file /home/call/MetaGT/metaGT/environment.yml
status : 143
message:

Aug-14 00:37:39.282 [Actor Thread 9] ERROR nextflow.processor.TaskProcessor - Error executing process > 'MINIMAP2 (1)'

Caused by:
Failed to create Conda environment
command: conda env create --prefix /home/call/MetaGT/work/conda/metaGT-1.0-f7c8dc3121d55495d60aeb53bd2259e3 --file /home/call/MetaGT/metaGT/environment.yml
status : 143
message:

java.lang.IllegalStateException: java.lang.IllegalStateException: Failed to create Conda environment
command: conda env create --prefix /home/call/MetaGT/work/conda/metaGT-1.0-f7c8dc3121d55495d60aeb53bd2259e3 --file /home/call/MetaGT/metaGT/environment.yml
status : 143
message:
"

I hope there is a solution to this problem

Best,
Cesar

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