ablab
'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
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metaGT v1.0dev
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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
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Only displaying parameters that differ from defaults.
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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
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
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
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
Dear @Lafmas
As far as I understand this warning does not affect the run, right? It sill completes despite the warning?
Best Andrey
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
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
Dear @andrewprzh
Sure. I will try it.
As soon as the results are confirmed, I will share them here
Best Lafmas
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
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
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
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
