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useMicromamba option doesn't work - generates Conda instructions instead. #4161

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jemma-nelson opened this issue Aug 7, 2023 · 10 comments · Fixed by #4302
Closed

useMicromamba option doesn't work - generates Conda instructions instead. #4161

jemma-nelson opened this issue Aug 7, 2023 · 10 comments · Fixed by #4302
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software/conda

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@jemma-nelson
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Bug report

Expected behavior and actual behavior

According to the docs, the useMicromamba directive should cause Nextflow to use Micromamba instead of Conda.

When using this option, the nextflow process fails to run, because the generated .command.run file still uses conda.

Steps to reproduce the problem

On a machine with micromamba installed, but not conda:

git clone https://gist.github.com/jemma-nelson/921e3a8aa32efe22bd73fbe1cbdfd09b
cd 921e3a8aa32efe22bd73fbe1cbdfd09b/
bash run.sh

Program output

The .nextflow.log file, as well as the generated .command.* files are in the gist referenced above. (e.g: https://gist.github.com/jemma-nelson/921e3a8aa32efe22bd73fbe1cbdfd09b#file-nextflow-log)

Program output:

N E X T F L O W  ~  version 23.04.2
Launching `main.nf` [nostalgic_ardinghelli] DSL2 - revision: e1ee91cb36
[-        ] process > greet -
Creating env using micromamba: /home/nelsonjs/tmp/repro-micromamba/test-repro/921e3a8aa32efe22bd73fbe1cbdfd09b/env.yaml [cache executor >  local (1)                                                                                                          [e2/667fd3] process > greet (1) [  0%] 0 of 1
executor >  local (1)                                                                                                          [e2/667fd3] process > greet (1) [  0%] 0 of 1                                                                                  executor >  local (1)                                                                                                          [e2/667fd3] process > greet (1) [100%] 1 of 1, failed: 1 ✘                                                                     Creating env using micromamba: /home/nelsonjs/tmp/repro-micromamba/test-repro/921e3a8aa32efe22bd73fbe1cbdfd09b/env.yaml [cache /home/nelsonjs/tmp/repro-micromamba/test-repro/921e3a8aa32efe22bd73fbe1cbdfd09b/work/conda/base-bda312ce1312db01eb3e5e99160dbdb1]
ERROR ~ Error executing process > 'greet (1)'

Caused by:
  Process `greet (1)` terminated with an error exit status (1)

Command executed:

  echo hello world

Command exit status:
  1

Command output:
  (empty)

Command error:
  .command.run: line 119: conda: command not found
  .command.run: line 119: /bin/activate: No such file or directory

Work dir:
  /home/nelsonjs/tmp/repro-micromamba/test-repro/921e3a8aa32efe22bd73fbe1cbdfd09b/work/e2/667fd3bde76e5bdf8df569044e15a6

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

 -- Check '.nextflow.log' file for details

Environment

  • Nextflow version: 23.04.2
  • Java version: java 11.0.16 2022-07-19 LTS
  • Operating system: Linux
  • Bash version: 4.2.46
  • Micromamba version: 1.4.7

Additional context

I mentioned this in slack last week, but did not get any attention. https://nextflow.slack.com/archives/C02T98A23U7/p1690325743801519

As near as I can tell from examining the source code, this configuration option cannot work, nor can the useMamba option, as nextflow always emits conda info --json for conda activation.

You may also want to add --yes to the micromamba create command, because if export MAMBA_ALWAYS_YES=true is not set, environment creation will hang indefinitely.
@bentsherman
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Fair enough, should be a simple fix. Fwiw, I've been using Mambaforge which provides mamba as a drop-in replacement for conda rather than a separate command, so that I don't have to bother with these settings.

@pditommaso
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pditommaso commented Aug 8, 2023 •
edited
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Do you mean miniforge? Not sure it's the same it says

conda-forge set as the default (and only) channel.

In any case the the support for micromamba should be honoured as described in the docs

@bentsherman
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Mambaforge is miniforge with mamba as the default conda backend. Not sure why it says conda-forge is the only channel because it allows any channels.

@pditommaso
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Unable to replicate. Nextflow uses micromamba with the provided test case

Caused by:
  Failed to create Conda environment
  command: micromamba env create --prefix /Users/pditommaso/Projects/921e3a8aa32efe22bd73fbe1cbdfd09b/work/conda/base-bda312ce1312db01eb3e5e99160dbdb1 --file /Users/pditommaso/Projects/921e3a8aa32efe22bd73fbe1cbdfd09b/env.yaml
  status : 127
  message:
    bash: micromamba: command not found

@bentsherman
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I think there is still a bug here though:

nextflow/modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy

Lines 430 to 437 in 7d6ad62

private String getCondaActivateSnippet() {
if( !condaEnv )
return null
def result = "# conda environment\n"
result += 'source $(conda info --json | awk \'/conda_prefix/ { gsub(/"|,/, "", $2); print $2 }\')'
result += "/bin/activate ${Escape.path(condaEnv)}\n"
return result
}

The problem was never that the conda builder doesn't use micromamba, but that the bash wrapper uses conda info to activate the environment. If you happen to have conda installed it may work, but if not, I wouldn't expect it to work. This error would happen when the task is executed.

@shenker
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shenker commented Sep 6, 2023

I can reproduce the two bugs discussed above:

  1. --yes should be added to the micromamba create command. Otherwise one needs to manually set the envvar MAMBA_ALWAYS_YES=true when running nextflow.
  2. The use of conda in the bash wrapper (as identified by @bentsherman above) needs to be replaced with micromamba. (A temporary workaround is to micromamba install conda, but nextflow should handle pure-micromamba installs, because pure-micromamba is probably the best practice for managing conda envs going forward.) To fix this, in line 434 of the above snippet, the conda/awk invocation can probably be replaced more simply by something like micromamba info|grep "env location :"|cut -d : -f 2.

Would be great to get a nextflow release that fixes these!

@bentsherman bentsherman reopened this Sep 6, 2023
@bentsherman
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Thanks @shenker . Regarding the -y option, it looks like it is already added in most cases:

nextflow/modules/nextflow/src/main/groovy/nextflow/conda/CondaCache.groovy

Lines 284 to 296 in 89ede15

def cmd
if( isYamlFilePath(condaEnv) ) {
final target = isYamlUriPath(condaEnv) ? condaEnv : Escape.path(makeAbsolute(condaEnv))
cmd = "${binaryName} env create --prefix ${Escape.path(prefixPath)} --file ${target}"
}
else if( isTextFilePath(condaEnv) ) {
cmd = "${binaryName} create ${opts}--yes --quiet --prefix ${Escape.path(prefixPath)} --file ${Escape.path(makeAbsolute(condaEnv))}"
}
else {
final channelsOpt = channels.collect(it -> "-c $it ").join('')
cmd = "${binaryName} create ${opts}--yes --quiet --prefix ${Escape.path(prefixPath)} ${channelsOpt}$condaEnv"
}

I think it is not added for conda env create because that command does not have a -y option. Is micromamba different?

@bentsherman bentsherman mentioned this issue Sep 13, 2023
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@shenker
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shenker commented Sep 13, 2023

Yes, micromamba env create accepts -y (it's confusing but the micromamba CLI is subtly different from the mamba/conda interfaces, the latter two being near-identical).

@ewels ewels mentioned this issue Sep 6, 2024
Closed
@ewels ewels mentioned this issue Oct 23, 2024
Merged
@ewels
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ewels commented Nov 8, 2024

Should be solved in #4302 and released in 24.10.0, however the following error + log was reported in the nf-core Slack. Looks like Mamba is requesting confirmation for the mamba env create command?

Caused by:
  Failed to create Conda environment
    command: mamba env create --prefix /path/to/conda/environment/cache/directory/environment-9b0544c1a5024cf208947cbaff805d06 --file /root/.nextflow/assets/nf-core/rnaseq/./subworkflows/loc
al/prepare_genome/../../../modules/local/gtf_filter/environment.yml
    status : 143
    message:
      Transaction
      
        Prefix: /path/to/conda/environment/cache/directory/environment-9b0544c1a5024cf208947cbaff805d06
      
        Updating specs:
      
         - conda-forge::python=3.9.5
      
      
        Package               Version  Build               Channel          Size
      ────────────────────────────────────────────────────────────────────────────
        Install:
      ────────────────────────────────────────────────────────────────────────────
      
        + _libgcc_mutex           0.1  conda_forge         conda-forge       3kB
        + _openmp_mutex           4.5  2_gnu               conda-forge      24kB
        + ca-certificates   2024.8.30  hbcca054_0          conda-forge     159kB
        + ld_impl_linux-64       2.43  h712a8e2_2          conda-forge     669kB
        + libffi                  3.3  h58526e2_2          conda-forge      53kB
        + libgcc               14.2.0  h77fa898_1          conda-forge     849kB
        + libgcc-ng            14.2.0  h69a702a_1          conda-forge      54kB
        + libgomp              14.2.0  h77fa898_1          conda-forge     461kB
        + libsqlite            3.46.0  hde9e2c9_0          conda-forge     865kB
        + libstdcxx            14.2.0  hc0a3c3a_1          conda-forge       4MB
        + libstdcxx-ng         14.2.0  h4852527_1          conda-forge      54kB
        + libzlib              1.2.13  h4ab18f5_6          conda-forge      62kB
        + ncurses                 6.5  he02047a_1          conda-forge     889kB
        + openssl              1.1.1w  hd590300_0          conda-forge       2MB
        + pip                  24.3.1  pyh8b19718_0        conda-forge       1MB
        + python                3.9.5  h49503c6_0_cpython  conda-forge      29MB
        + readline                8.2  h8228510_1          conda-forge     281kB
        + setuptools           75.3.0  pyhd8ed1ab_0        conda-forge     780kB
        + sqlite               3.46.0  h6d4b2fc_0          conda-forge     860kB
        + tk                   8.6.13  noxft_h4845f30_101  conda-forge       3MB
        + tzdata                2024b  hc8b5060_0          conda-forge     122kB
        + wheel                0.44.0  pyhd8ed1ab_0        conda-forge      59kB
        + xz                    5.2.6  h166bdaf_0          conda-forge     418kB
        + zlib                 1.2.13  h4ab18f5_6          conda-forge      93kB
                                                                                                                                                                                     [293/695]
        Summary:
      
        Install: 24 packages
      
        Total download: 46MB
      
      ────────────────────────────────────────────────────────────────────────────
      
      
      Confirm changes: [Y/n]
Full output 
nextflow run nf-core/rnaseq -r 3.17.0 -profile test,mamba --outdir lol                                                                     [691/695]
                                                                                                                                                                                              
 N E X T F L O W   ~  version 24.10.0                                                                                                                                                         
                                                                                                                                                                                              
Launching `https://github.com/nf-core/rnaseq` [pensive_meucci] DSL2 - revision: 00f924cf92 [3.17.0]                                                                                           
                                                                                                                                                                                              
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                                                                                                          
    There is a problem with your Conda configuration!                                                                                                                                         
    You will need to set-up the conda-forge and bioconda channels correctly.                                                                                                                  
    Please refer to https://bioconda.github.io/                                                                                                                                               
    The observed channel order is                                                                                                                                                             
    [defaults]                                                                                                                                                                                
    but the following channel order is required:                                                                                                                                              
    [conda-forge, bioconda]                                                                                                                                                                   
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"                                                                                                          
                                                                                                                                                                                              
                                                                                                                                                                                              
------------------------------------------------------                                                                                                                                        
                                        ,--./,-.                                                                                                                                              
        ___     __   __   __   ___     /,-._.--~'                                                                                                                                             
  |\ | |__  __ /  ` /  \ |__) |__         }  {                                                                                                                                                
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,                                                                                                                                             
                                        `._,._,'                                                                                                                                              
  nf-core/rnaseq 3.17.0                                                                                                                                                                       
------------------------------------------------------                                                                                                                                        
Input/output options                                                                                                                                                                          
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv                         
  outdir                    : lol                                                                                                                                                             
                                                                                                                                                                                              
Reference genome options                                                                                                                                                                      
  fasta                     : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genome.fasta                                         
  gtf                       : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes_with_empty_tid.gtf.gz                          
  gff                       : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes.gff.gz                                         
  transcript_fasta          : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/transcriptome.fasta                                  
  additional_fasta          : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/gfp.fa.gz                                            
  hisat2_index              : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/hisat2.tar.gz                                        
  rsem_index                : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/rsem.tar.gz                                          
  salmon_index              : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/salmon.tar.gz                                        
                                                                                                                                                                                              
Read filtering options                                                                                                                                                                        
  bbsplit_fasta_list        : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/bbsplit_fasta_list.txt                               
UMI options
  umitools_bc_pattern       : NNNN
                                                                                                                                                                                    [647/695]
Alignment options
  pseudo_aligner            : salmon
  min_mapped_reads          : 5
Process skipping options
  skip_bbsplit              : false
Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function
Core Nextflow options
  revision                  : 3.17.0
  runName                   : pensive_meucci
  launchDir                 : /common/workdir
  workDir                   : /common/workdir/work
  projectDir                : /root/.nextflow/assets/nf-core/rnaseq
  userName                  : root
  profile                   : test,mamba
  configFiles               : 
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The pipeline
    https://doi.org/10.5281/zenodo.1400710
* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
    https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Both '--gtf' and '--gff' parameters have been provided.
  Using GTF file as priority.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  '--transcript_fasta' parameter has been provided.
  Make sure transcript names in this file match those in the GFF/GTF file.
  Please see:
  https://github.com/nf-core/rnaseq/issues/753
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
executor >  local (7)                                                                                                                                                                [603/695]
[99/441716] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)                                                       [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER                                                                                     -
[c9/2ef0c7] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)                                                            [  0%] 0 of 1
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA                                                                      -
executor >  local (7)                                                                           
[99/441716] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)                                                       [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER                                                                                     -
[c9/2ef0c7] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)                                                            [  0%] 0 of 1
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA                                                                      -
executor >  local (7)                                                                           
[99/441716] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)                                                       [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER                                                                                     -
[c9/2ef0c7] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)                                                            [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA                                                                      -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED                                                                                        -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES                                                                           -
executor >  local (9)                                                                           
[99/441716] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)                                                       [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER                                                                                     -
[c9/2ef0c7] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)                                                            [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA                                                                      -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED                                                                                        -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES                                                                           -
executor >  local (9)                                                                           
[99/441716] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)                                                       [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER                                                                                     -
[c9/2ef0c7] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)                                                            [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA                                                                      -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED                                                                                        -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES                                                                           -
executor >  local (9)                                                                           
[99/441716] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)                                                       [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER                                                                                     -
[c9/2ef0c7] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)                                                            [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA                                                                      -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED                                                                                        -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES                                                                           -
executor >  local (9)                                                                           
[99/441716] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)                                                       [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER                                                                                     -
[c9/2ef0c7] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)                                                            [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA                                                                      -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED                                                                                        -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES                                                                           -
executor >  local (9)                                                                                                                                                                [558/695]
[99/441716] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)                                                       [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER                                                                                     -
[c9/2ef0c7] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)                                                            [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA                                                                      -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED                                                                                        -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES                                                                           -
executor >  local (9)                                                                           
[99/441716] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)                                                       [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER                                                                                     -
[c9/2ef0c7] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)                                                            [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA                                                                      -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED                                                                                        -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES                                                                           -
executor >  local (9)                                                                           
[99/441716] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)                                                       [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER                                                                                     -
[c9/2ef0c7] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)                                                            [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA                                                                      -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED                                                                                        -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES                                                                           -
executor >  local (9)                                                                           
[99/441716] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)                                                       [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER                                                                                     -
[c9/2ef0c7] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)                                                            [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA                                                                      -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED                                                                                        -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES                                                                           -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT                                                                                  -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE                                                                            -
[ad/206a40] process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)                                                             [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ                                                         -
[f9/a40fd5] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)                 [100%] 3 of 3
[13/3dc6d3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)             [100%] 3 of 3
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT                                                     -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE                            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT                            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN                                                                                  -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT                                                       -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS                                   -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT                                -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS                                -
executor >  local (9)                                                                           
[99/441716] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)                                           [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER                                                                         -                                              [513/695]
[c9/2ef0c7] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)                                                [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA                                                          -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED                                                                            -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES                                                               -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT                                                                      -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE                                                                -
[ad/206a40] process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)                                                 [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ                                             -
[f9/a40fd5] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)     [100%] 3 of 3
[13/3dc6d3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2) [100%] 3 of 3
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT                                         -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE                -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT                -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN                                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT                                           -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX                                          -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS                       -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT                    -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS                    -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT                                                          -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE                                                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE                                                               -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED                                                 -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED                                                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT                                                         -
[-        ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON                                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES                                            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX                                                   -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS                                -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT                             -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS                             -
[-        ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE                                                                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS                                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE                                                                     -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW                                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV                                                                     -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP                                     -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG                            -
Plus 20 more processes waiting for tasks…
                                                                                                                                                                                   [472/695]
ERROR ~ Error executing process > 'NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER'
Caused by:
  Failed to create Conda environment
    command: mamba env create --prefix /path/to/conda/environment/cache/directory/environment-9b0544c1a5024cf208947cbaff805d06 --file /root/.nextflow/assets/nf-core/rnaseq/./subworkflows/loc
al/prepare_genome/../../../modules/local/gtf_filter/environment.yml
    status : 143
    message:
      Transaction
      
        Prefix: /path/to/conda/environment/cache/directory/environment-9b0544c1a5024cf208947cbaff805d06
      
        Updating specs:
      
         - conda-forge::python=3.9.5
      
      
        Package               Version  Build               Channel          Size
executor >  local (9)                           
[99/441716] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)                                           [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER                                                                         -
[c9/2ef0c7] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)                                                [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA                                                          -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED                                                                            -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES                                                               -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT                                                                      -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE                                                                -
[ad/206a40] process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)                                                 [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ                                             -
[f9/a40fd5] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)     [100%] 3 of 3
[13/3dc6d3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2) [100%] 3 of 3
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT                                         -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE                -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT                -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN                                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT                                           -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX                                          -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS                       -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT                    -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS                    -

[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT                                                          -                                              [427/695]
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE                                                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE                                                               -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED                                                 -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED                                                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT                                                         -
[-        ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON                                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES                                            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX                                                   -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS                                -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT                             -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS                             -
[-        ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE                                                                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS                                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE                                                                     -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW                                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV                                                                     -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP                                     -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG                            -
Plus 20 more processes waiting for tasks…
ERROR ~ Error executing process > 'NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER'
Caused by:
  Failed to create Conda environment
    command: mamba env create --prefix /path/to/conda/environment/cache/directory/environment-9b0544c1a5024cf208947cbaff805d06 --file /root/.nextflow/assets/nf-core/rnaseq/./subworkflows/loc
al/prepare_genome/../../../modules/local/gtf_filter/environment.yml
    status : 143
    message:
      Transaction
      
        Prefix: /path/to/conda/environment/cache/directory/environment-9b0544c1a5024cf208947cbaff805d06
      
        Updating specs:
      
         - conda-forge::python=3.9.5
      
      
        Package               Version  Build               Channel          Size
      ────────────────────────────────────────────────────────────────────────────
        Install:
      ────────────────────────────────────────────────────────────────────────────
      
        + _libgcc_mutex           0.1  conda_forge         conda-forge       3kB
        + _openmp_mutex           4.5  2_gnu               conda-forge      24kB

executor >  local (9)                                                                                                                                                                [382/695]
[99/441716] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)                                           [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER                                                                         -
[c9/2ef0c7] process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)                                                [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA                                                          -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED                                                                            -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES                                                               -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT                                                                      -
[-        ] process > NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE                                                                -
[ad/206a40] process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)                                                 [100%] 1 of 1 ✔
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ                                             -
[f9/a40fd5] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)     [100%] 3 of 3
[13/3dc6d3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2) [100%] 3 of 3
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT                                         -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE                -
[-        ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT                -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN                                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT                                           -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX                                          -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS                       -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT                    -
[-        ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS                    -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT                                                          -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE                                                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE                                                               -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED                                                 -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED                                                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT                                                         -
[-        ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON                                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES                                            -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX                                                   -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS                                -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT                             -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS                             -
[-        ] process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE                                                                        -
[-        ] process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS                                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE                                                                     -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW                                                                      -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV                                                                     -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP                                     -
[-        ] process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG                            -
Plus 20 more processes waiting for tasks…       
ERROR ~ Error executing process > 'NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER'

                                                                                                                                                                                    [338/695]
Caused by:
  Failed to create Conda environment
    command: mamba env create --prefix /path/to/conda/environment/cache/directory/environment-9b0544c1a5024cf208947cbaff805d06 --file /root/.nextflow/assets/nf-core/rnaseq/./subworkflows/loc
al/prepare_genome/../../../modules/local/gtf_filter/environment.yml
    status : 143
    message:
      Transaction
      
        Prefix: /path/to/conda/environment/cache/directory/environment-9b0544c1a5024cf208947cbaff805d06
      
        Updating specs:
      
         - conda-forge::python=3.9.5
      
      
        Package               Version  Build               Channel          Size
      ────────────────────────────────────────────────────────────────────────────
        Install:
      ────────────────────────────────────────────────────────────────────────────
      
        + _libgcc_mutex           0.1  conda_forge         conda-forge       3kB
        + _openmp_mutex           4.5  2_gnu               conda-forge      24kB
        + ca-certificates   2024.8.30  hbcca054_0          conda-forge     159kB
        + ld_impl_linux-64       2.43  h712a8e2_2          conda-forge     669kB
        + libffi                  3.3  h58526e2_2          conda-forge      53kB
        + libgcc               14.2.0  h77fa898_1          conda-forge     849kB
        + libgcc-ng            14.2.0  h69a702a_1          conda-forge      54kB
        + libgomp              14.2.0  h77fa898_1          conda-forge     461kB
        + libsqlite            3.46.0  hde9e2c9_0          conda-forge     865kB
        + libstdcxx            14.2.0  hc0a3c3a_1          conda-forge       4MB
        + libstdcxx-ng         14.2.0  h4852527_1          conda-forge      54kB
        + libzlib              1.2.13  h4ab18f5_6          conda-forge      62kB
        + ncurses                 6.5  he02047a_1          conda-forge     889kB
        + openssl              1.1.1w  hd590300_0          conda-forge       2MB
        + pip                  24.3.1  pyh8b19718_0        conda-forge       1MB
        + python                3.9.5  h49503c6_0_cpython  conda-forge      29MB
        + readline                8.2  h8228510_1          conda-forge     281kB
        + setuptools           75.3.0  pyhd8ed1ab_0        conda-forge     780kB
        + sqlite               3.46.0  h6d4b2fc_0          conda-forge     860kB
        + tk                   8.6.13  noxft_h4845f30_101  conda-forge       3MB
        + tzdata                2024b  hc8b5060_0          conda-forge     122kB
        + wheel                0.44.0  pyhd8ed1ab_0        conda-forge      59kB
        + xz                    5.2.6  h166bdaf_0          conda-forge     418kB
        + zlib                 1.2.13  h4ab18f5_6          conda-forge      93kB
                                                                                                                                                                                     [293/695]
        Summary:
      
        Install: 24 packages
      
        Total download: 46MB
      
      ────────────────────────────────────────────────────────────────────────────
      
      
      Confirm changes: [Y/n]
 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
 -- Check '.nextflow.log' file for details

mamba version is 2.0.3
Rocky Linux 8.7 x86_64

@jemma-nelson
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You may be able to use the workaround described here: #4161 (comment) - set export MAMBA_ALWAYS_YES=true in your shell environment. (if you are not using bash, the process for defining/exporting a environment variable may be different).

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Add fallback command for micromamba nextflow-io/nextflow
5 participants
@shenker @ewels @pditommaso @bentsherman @jemma-nelson