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Python/minimap2 not found when running v2.3.0 using Singularity on demo data #144

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gabyrech opened this issue Oct 26, 2024 · 8 comments
Open

Python/minimap2 not found when running v2.3.0 using Singularity on demo data #144

gabyrech opened this issue Oct 26, 2024 · 8 comments

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@gabyrech
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Operating System

Other Linux (please specify below)

Other Linux

Rocky9

Workflow Version

v2.3.0

Workflow Execution

Command line (Cluster)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

$ nextflow run epi2me-labs/wf-single-cell -revision 'v2.3.0' -profile singularity --threads '24' --expected_cells 100 --fastq 'wf-single-cell-demo/chr17.fq.gz' --kit '3prime:v3' --ref_genome_dir 'wf-single-cell-demo' --genes_of_interest 'wf-single-cell-demo/umap_plot_genes.csv' --out_dir test_wf-single-cell

Workflow Execution - CLI Execution Profile

None

What happened?

I am getting different errors related with software not found when running using singularly profile. I am copying in this issue the output for one of the cases in which I get 'python: command not found' but I am also getting 'minimap2: command not found' on a different attempt.

ERROR ~ Error executing process > 'pipeline:preprocess:build_minimap_index'
  .command.sh: line 2: minimap2: command not found

Not sure if this is related, but when running v2.3.0 it strikes me that is pulling singularity image ontresearch-wf-single-cell-sha0fcdf10929fbef2d426bb985e16b81153a88c6f4.img which is a 6 months old image in your docker hub.

Relevant log output

--------------------------------------------------------------------------------
This is epi2me-labs/wf-single-cell v2.3.0-gea5d3c0.
--------------------------------------------------------------------------------
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
[-        ] process > fastcat                                       -
[-        ] process > parse_kit_metadata                            -
[-        ] process > pipeline:getVersions                          -
[-        ] process > pipeline:getParams                            -
[-        ] process > pipeline:preprocess:call_paftools             -
[-        ] process > pipeline:preprocess:build_minimap_index       -
[-        ] process > pipeline:preprocess:call_adapter_scan         -
[-        ] process > pipeline:preprocess:summarize_adapter_table   -
[-        ] process > pipeline:process_bams:split_gtf_by_chroms     -
[-        ] process > pipeline:process_bams:generate_whitelist      -
executor >  local (6)
[40/c81908] process > fastcat (1)                                   [  0%] 0 of 1
[-        ] process > parse_kit_metadata                            -
[2f/efde54] process > pipeline:getVersions                          [  0%] 0 of 1
[10/dfe022] process > pipeline:getParams                            [  0%] 0 of 1
[9b/736e2f] process > pipeline:preprocess:call_paftools             [  0%] 0 of 1
[58/627727] process > pipeline:preprocess:build_minimap_index       [  0%] 0 of 1
[-        ] process > pipeline:preprocess:call_adapter_scan         -
[-        ] process > pipeline:preprocess:summarize_adapter_table   -
[2b/c1b228] process > pipeline:process_bams:split_gtf_by_chroms     [  0%] 0 of 1
[-        ] process > pipeline:process_bams:generate_whitelist      -
executor >  local (6)
[40/c81908] process > fastcat (1)                                   [  0%] 0 of 1
[-        ] process > parse_kit_metadata                            -
[2f/efde54] process > pipeline:getVersions                          [  0%] 0 of 1
[10/dfe022] process > pipeline:getParams                            [  0%] 0 of 1
[9b/736e2f] process > pipeline:preprocess:call_paftools             [  0%] 0 of 1
[58/627727] process > pipeline:preprocess:build_minimap_index       [  0%] 0 of 1
[-        ] process > pipeline:preprocess:call_adapter_scan         -
[-        ] process > pipeline:preprocess:summarize_adapter_table   -
[2b/c1b228] process > pipeline:process_bams:split_gtf_by_chroms     [  0%] 0 of 1
[-        ] process > pipeline:process_bams:generate_whitelist      -
[-        ] process > pipeline:process_bams:assign_barcodes         -
[-        ] process > pipeline:process_bams:cat_tags_by_chrom       -
[-        ] process > pipeline:process_bams:merge_bams              -
[-        ] process > pipeline:process_bams:stringtie               -
[-        ] process > pipeline:process_bams:align_to_transcriptome  -
[-        ] process > pipeline:process_bams:assign_features         -
[-        ] process > pipeline:process_bams:create_matrix           -
[-        ] process > pipeline:process_bams:process_matrix          -
[-        ] process > pipeline:process_bams:merge_transcriptome     -
[-        ] process > pipeline:process_bams:combine_final_tag_files -
[-        ] process > pipeline:process_bams:tag_bam                 -
[-        ] process > pipeline:process_bams:umi_gene_saturation     -
[-        ] process > pipeline:process_bams:pack_images             -
[-        ] process > pipeline:prepare_report_data                  -
[-        ] process > pipeline:makeReport                           -
ERROR ~ Error executing process > 'pipeline:getVersions'

Caused by:
  Process `pipeline:getVersions` terminated with an error exit status (127)

Command executed:

  python -c "import pysam; print(f'pysam,{pysam.__version__}')" >> versions.txt
  python -c "import parasail; print(f'parasail,{parasail.__version__}')" >> versions.txt
  python -c "import pandas; print(f'pandas,{pandas.__version__}')" >> versions.txt
  python -c "import rapidfuzz; print(f'rapidfuzz,{rapidfuzz.__version__}')" >> versions.txt
  python -c "import sklearn; print(f'scikit-learn,{sklearn.__version__}')" >> versions.txt
  fastcat --version | sed 's/^/fastcat,/' >> versions.txt
  minimap2 --version | sed 's/^/minimap2,/' >> versions.txt
  samtools --version | head -n 1 | sed 's/ /,/' >> versions.txt
  bedtools --version | head -n 1 | sed 's/ /,/' >> versions.txt
  gffread --version | sed 's/^/gffread,/' >> versions.txt
  seqkit version | head -n 1 | sed 's/ /,/' >> versions.txt
  stringtie --version | sed 's/^/stringtie,/' >> versions.txt
  gffcompare --version | head -n 1 | sed 's/ /,/' >> versions.txt

Command exit status:
  127

Command output:
executor >  local (6)
[40/c81908] process > fastcat (1)                                   [  0%] 0 of 1
[-        ] process > parse_kit_metadata                            -
[2f/efde54] process > pipeline:getVersions                          [100%] 1 of 1, failed: 1 ✘
[10/dfe022] process > pipeline:getParams                            [100%] 1 of 1 ✔
[9b/736e2f] process > pipeline:preprocess:call_paftools             [100%] 1 of 1, failed: 1 ✘
[58/627727] process > pipeline:preprocess:build_minimap_index       [  0%] 0 of 1
[-        ] process > pipeline:preprocess:call_adapter_scan         -
[-        ] process > pipeline:preprocess:summarize_adapter_table   -
[2b/c1b228] process > pipeline:process_bams:split_gtf_by_chroms     [100%] 1 of 1, failed: 1 ✘
[-        ] process > pipeline:process_bams:generate_whitelist      -
[-        ] process > pipeline:process_bams:assign_barcodes         -
[-        ] process > pipeline:process_bams:cat_tags_by_chrom       -
[-        ] process > pipeline:process_bams:merge_bams              -
[-        ] process > pipeline:process_bams:stringtie               -
[-        ] process > pipeline:process_bams:align_to_transcriptome  -
[-        ] process > pipeline:process_bams:assign_features         -
[-        ] process > pipeline:process_bams:create_matrix           -
[-        ] process > pipeline:process_bams:process_matrix          -
[-        ] process > pipeline:process_bams:merge_transcriptome     -
[-        ] process > pipeline:process_bams:combine_final_tag_files -
[-        ] process > pipeline:process_bams:tag_bam                 -
[-        ] process > pipeline:process_bams:umi_gene_saturation     -
[-        ] process > pipeline:process_bams:pack_images             -
[-        ] process > pipeline:prepare_report_data                  -
[-        ] process > pipeline:makeReport                           -
ERROR ~ Error executing process > 'pipeline:getVersions'

Caused by:
  Process `pipeline:getVersions` terminated with an error exit status (127)

Command executed:

  python -c "import pysam; print(f'pysam,{pysam.__version__}')" >> versions.txt
  python -c "import parasail; print(f'parasail,{parasail.__version__}')" >> versions.txt
  python -c "import pandas; print(f'pandas,{pandas.__version__}')" >> versions.txt
  python -c "import rapidfuzz; print(f'rapidfuzz,{rapidfuzz.__version__}')" >> versions.txt
  python -c "import sklearn; print(f'scikit-learn,{sklearn.__version__}')" >> versions.txt
  fastcat --version | sed 's/^/fastcat,/' >> versions.txt
  minimap2 --version | sed 's/^/minimap2,/' >> versions.txt
  samtools --version | head -n 1 | sed 's/ /,/' >> versions.txt
  bedtools --version | head -n 1 | sed 's/ /,/' >> versions.txt
  gffread --version | sed 's/^/gffread,/' >> versions.txt
  seqkit version | head -n 1 | sed 's/ /,/' >> versions.txt
  stringtie --version | sed 's/^/stringtie,/' >> versions.txt
  gffcompare --version | head -n 1 | sed 's/ /,/' >> versions.txt

Command exit status:
  127

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  INFO:    underlay of /etc/localtime required more than 50 (78) bind mounts
  .command.sh: line 2: python: command not found

Work dir:
  /XX/YYYY/rechg/nextflow/work/2f/efde54ed04aa5707114adc5ece1d11

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
WARN: Killing running tasks (2)

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

no

Other demo data information

No response
@nrhorner
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Contributor

nrhorner commented Nov 5, 2024

Hi @gabyrech

Are you able to run the container directly? What happens when you do the following?

singularity shell docker://ontresearch/wf-single-cell:sha0fcdf10929fbef2d426bb985e16b81153a88c6f4
minimap2

@gabyrech
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gabyrech commented Nov 5, 2024

Hi @nrhorner , thanks for your reply. Nope, that doesn't work neither:

$ singularity shell docker://ontresearch/wf-single-cell:sha0fcdf10929fbef2d426bb985e16b81153a88c6f4
INFO:    Environment variable SINGULARITY_BIND is set, but APPTAINER_BIND is preferred
INFO:    Using cached SIF image
INFO:    underlay of /etc/localtime required more than 50 (78) bind mounts
Apptainer> minimap2
bash: minimap2: command not found
Apptainer>

@nrhorner
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nrhorner commented Nov 6, 2024

Hi @gabyrech

In the container, do you have this folder and is minimap2 in there? /home/epi2melabs/conda/bin

@nrhorner
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nrhorner commented Nov 6, 2024

Also could you try to see if other containers work for you or not.

singularity shell docker://nanozoo/minimap2
minimap2

@gabyrech
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gabyrech commented Nov 7, 2024

Hi @nrhorner ,

Ok, it seems like that directory is not mounted in the container:

$ singularity shell docker://ontresearch/wf-single-cell:sha0fcdf10929fbef2d426bb985e16b81153a88c6f4
INFO:    Environment variable SINGULARITY_BIND is set, but APPTAINER_BIND is preferred
INFO:    Using cached SIF image
INFO:    underlay of /etc/localtime required more than 50 (78) bind mounts
Apptainer> cd /home/epi2melabs/conda/bin
bash: cd: /home/epi2melabs/conda/bin: No such file or directory
Apptainer> cd /home/epi2melabs
bash: cd: /home/epi2melabs: No such file or directory

minimap2 container seems to work ok:

$ singularity shell docker://nanozoo/minimap2
INFO:    Environment variable SINGULARITY_BIND is set, but APPTAINER_BIND is preferred
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob 68ced04f60ab done
Copying blob 96cf53b3a9dd done
Copying blob 9c388eb6d33c done
Copying blob 53301a2590b2 done
Copying blob 674acdf01132 done
Copying blob 33f70366784c done
Copying config 002ee85391 done
Writing manifest to image destination
Storing signatures
2024/11/06 21:34:13  info unpack layer: sha256:68ced04f60ab5c7a5f1d0b0b4e7572c5a4c8cce44866513d30d9df1a15277d6b
2024/11/06 21:34:14  info unpack layer: sha256:9c388eb6d33c40662539172f0d9a357287bd1cd171692ca5c08db2886bc527c3
2024/11/06 21:34:16  info unpack layer: sha256:96cf53b3a9dd496f4c91ab86eeadca2c8a31210c2e5c2a82badbb0dcf8c8f76b
2024/11/06 21:34:18  info unpack layer: sha256:674acdf01132de9db11b3ca44fb4b3c2a3507906d8f846f0260d345c61cd4d0a
2024/11/06 21:34:18  info unpack layer: sha256:33f70366784c85746fbb8f637775a7b62f082468d0e05b08fb1365a0d6673014
2024/11/06 21:34:18  info unpack layer: sha256:53301a2590b2101e785e76947547cbf4d96480a80d9b6c32b7eb046e79941c79
INFO:    Creating SIF file...
Apptainer> minimap2 --version
2.17-r941

@gabyrech
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Any updates on this issue? we are seeing the same for other epi2me workflows as well.. Just wondering if is a something at our end... Any ideas on what could be?

@cjw85
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cjw85 commented Nov 25, 2024

This looks like a conflict between our container images and your singularity setup.

Our containers contain data at a path /home/epi2melabs/. I suspect your singularity is setup to automatically mount your /home from your host operating system into the running container, which ends up stomping on the existing /home of the container image.

Depending on your singularity/apptainer version you may have a --no-mount or a --no-home option to singularity which can be used to disable this behaviour. You can try creating a nextflow configuration file with:

# file named my_config.cfg
profiles {
    my_singularity {
        singularity {
            enabled = true
            autoMounts = true
            engineOptions = "--no-home"
        }
    }
}

and then run nextflow with:

nextflow run epi2me-labs/wf-single-cell -C my_config.cfg -profile my_singularity ....

@gabyrech
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Thank you @cjw85,
Ok, I think I getting closer. Now I am getting a different error. I get essentialy the same error either with --no-mount or --no-home

$ cat epi2me_config.cfg
profiles {
    my_singularity {
        singularity {
            enabled = true
            autoMounts = true
            engineOptions = "--no-home"
        }
    }
}

$ nextflow run epi2me-labs/wf-single-cell -c epi2me_config.cfg -revision 'v2.3.0' -profile my_singularity --threads '24' --expected_cells 100 --fastq 'wf-single-cell-demo/chr17.fq.gz' --kit '3prime:v3' --ref_genome_dir 'wf-single-cell-demo' --genes_of_interest 'wf-single-cell-demo/umap_plot_genes.csv' --out_dir test_wf-single-cell

N E X T F L O W  ~  version 23.04.4
Launching `https://github.com/epi2me-labs/wf-single-cell` [marvelous_leibniz] DSL2 - revision: ea5d3c0251 [v2.3.0]
||||||||||   _____ ____ ___ ____  __  __ _____      _       _
||||||||||  | ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
|||||       |  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
|||||       | |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
||||||||||  |_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
||||||||||  wf-single-cell v2.3.0-gea5d3c0
--------------------------------------------------------------------------------
Core Nextflow options
  revision         : v2.3.0
  runName          : marvelous_leibniz
  containerEngine  : singularity
  launchDir        : /xx/yyy/user/nextflow
  workDir          : /xx/yyy/user/nextflow/work
  projectDir       : /xx/yyy/user/nextflow/assets/epi2me-labs/wf-single-cell
  userName         : XXXX
  profile          : my_singularity
  configFiles      : /xx/yyy/user/nextflow/assets/epi2me-labs/wf-single-cell/nextflow.config, /xx/yyy/user/nextflow/epi2me_config.cfg

Input Options
  fastq            : wf-single-cell-demo/chr17.fq.gz
  ref_genome_dir   : wf-single-cell-demo
  expected_cells   : 100

Output Options
  out_dir          : test_wf-single-cell

Advanced options
  threads          : 24
  genes_of_interest: wf-single-cell-demo/umap_plot_genes.csv

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

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


--------------------------------------------------------------------------------
This is epi2me-labs/wf-single-cell v2.3.0-gea5d3c0.
--------------------------------------------------------------------------------
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
executor >  local (6)
[dc/192083] process > fastcat (1)                                   [  0%] 0 of 1
[-        ] process > parse_kit_metadata                            -
[00/08e8d8] process > pipeline:getVersions                          [  0%] 0 of 1
[50/d7d3d9] process > pipeline:getParams                            [  0%] 0 of 1
[6d/c8a7f5] process > pipeline:preprocess:call_paftools             [  0%] 0 of 1
[ab/249a5b] process > pipeline:preprocess:build_minimap_index       [  0%] 0 of 1
[-        ] process > pipeline:preprocess:call_adapter_scan         -
[-        ] process > pipeline:preprocess:summarize_adapter_table   -
[57/d972cf] process > pipeline:process_bams:split_gtf_by_chroms     [  0%] 0 of 1
[-        ] process > pipeline:process_bams:generate_whitelist      -
[-        ] process > pipeline:process_bams:assign_barcodes         -
[-        ] process > pipeline:process_bams:cat_tags_by_chrom       -
[-        ] process > pipeline:process_bams:merge_bams              -
[-        ] process > pipeline:process_bams:stringtie               -
[-        ] process > pipeline:process_bams:align_to_transcriptome  -
[-        ] process > pipeline:process_bams:assign_features         -
[-        ] process > pipeline:process_bams:create_matrix           -
[-        ] process > pipeline:process_bams:process_matrix          -
[-        ] process > pipeline:process_bams:merge_transcriptome     -
[-        ] process > pipeline:process_bams:combine_final_tag_files -
[-        ] process > pipeline:process_bams:tag_bam                 -
[-        ] process > pipeline:process_bams:umi_gene_saturation     -
[-        ] process > pipeline:process_bams:pack_images             -
[-        ] process > pipeline:prepare_report_data                  -
[-        ] process > pipeline:makeReport                           -
ERROR ~ Error executing process > 'fastcat (1)'

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

Command executed:

  mkdir fastcat_stats
  mkdir fastq_chunks

  # Save file as compressed fastq
  fastcat         -s chr17         -f fastcat_stats/per-file-stats.tsv         -i fastcat_stats/per-file-runids.tsv         -l fastcat_stats/per-file-basecallers.tsv         --histograms histograms                           input_src     | if [ "1000000" = "0" ]; then
      bgzip -@ 4 > fastq_chunks/seqs.fastq.gz
    else
      split -l 4000000 -d --additional-suffix=.fastq.gz --filter='bgzip -@ 4 > $FILE' - fastq_chunks/seqs_;
    fi

  mv histograms/* fastcat_stats

  # get n_seqs from per-file stats - need to sum them up
  awk 'NR==1{for (i=1; i<=NF; i++) {ix[$i] = i}} NR>1 {c+=$ix["n_seqs"]} END{print c}'         fastcat_stats/per-file-stats.tsv > fastcat_stats/n_seqs
  # get unique run IDs (we add `-F '\t'` as `awk` uses any stretch of whitespace
  # as field delimiter per default and thus ignores empty columns)
  awk -F '\t' '
      NR==1 {for (i=1; i<=NF; i++) {ix[$i] = i}}
      # only print run_id if present
      NR>1 && $ix["run_id"] != "" {print $ix["run_id"]}
  ' fastcat_stats/per-file-runids.tsv | sort | uniq > fastcat_stats/run_ids
  # get unique basecall models
  awk -F '\t' '
      NR==1 {for (i=1; i<=NF; i++) {ix[$i] = i}}
      # only print basecall model if present
      NR>1 && $ix["basecaller"] != "" {print $ix["basecaller"]}
  ' fastcat_stats/per-file-basecallers.tsv | sort | uniq > fastcat_stats/basecallers

Command exit status:
  1

Command output:
  (empty)

executor >  local (6)
[dc/192083] process > fastcat (1)                                   [100%] 1 of 1, failed: 1 ✘
[-        ] process > parse_kit_metadata                            -
[00/08e8d8] process > pipeline:getVersions                          [100%] 1 of 1, failed: 1 ✘
[50/d7d3d9] process > pipeline:getParams                            [100%] 1 of 1, failed: 1 ✘
[6d/c8a7f5] process > pipeline:preprocess:call_paftools             [100%] 1 of 1, failed: 1 ✘
[ab/249a5b] process > pipeline:preprocess:build_minimap_index       [100%] 1 of 1, failed: 1 ✘
[-        ] process > pipeline:preprocess:call_adapter_scan         -
[-        ] process > pipeline:preprocess:summarize_adapter_table   -
[57/d972cf] process > pipeline:process_bams:split_gtf_by_chroms     [100%] 1 of 1, failed: 1 ✘
[-        ] process > pipeline:process_bams:generate_whitelist      -
[-        ] process > pipeline:process_bams:assign_barcodes         -
[-        ] process > pipeline:process_bams:cat_tags_by_chrom       -
[-        ] process > pipeline:process_bams:merge_bams              -
[-        ] process > pipeline:process_bams:stringtie               -
[-        ] process > pipeline:process_bams:align_to_transcriptome  -
[-        ] process > pipeline:process_bams:assign_features         -
[-        ] process > pipeline:process_bams:create_matrix           -
[-        ] process > pipeline:process_bams:process_matrix          -
[-        ] process > pipeline:process_bams:merge_transcriptome     -
[-        ] process > pipeline:process_bams:combine_final_tag_files -
[-        ] process > pipeline:process_bams:tag_bam                 -
[-        ] process > pipeline:process_bams:umi_gene_saturation     -
[-        ] process > pipeline:process_bams:pack_images             -
[-        ] process > pipeline:prepare_report_data                  -
[-        ] process > pipeline:makeReport                           -
ERROR ~ Error executing process > 'fastcat (1)'

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

Command executed:

  mkdir fastcat_stats
  mkdir fastq_chunks

  # Save file as compressed fastq
  fastcat         -s chr17         -f fastcat_stats/per-file-stats.tsv         -i fastcat_stats/per-file-runids.tsv         -l fastcat_stats/per-file-basecallers.tsv         --histograms histograms                           input_src     | if [ "1000000" = "0" ]; then
      bgzip -@ 4 > fastq_chunks/seqs.fastq.gz
    else
      split -l 4000000 -d --additional-suffix=.fastq.gz --filter='bgzip -@ 4 > $FILE' - fastq_chunks/seqs_;
    fi

  mv histograms/* fastcat_stats

  # get n_seqs from per-file stats - need to sum them up
  awk 'NR==1{for (i=1; i<=NF; i++) {ix[$i] = i}} NR>1 {c+=$ix["n_seqs"]} END{print c}'         fastcat_stats/per-file-stats.tsv > fastcat_stats/n_seqs
  # get unique run IDs (we add `-F '\t'` as `awk` uses any stretch of whitespace
  # as field delimiter per default and thus ignores empty columns)
  awk -F '\t' '
      NR==1 {for (i=1; i<=NF; i++) {ix[$i] = i}}
      # only print run_id if present
      NR>1 && $ix["run_id"] != "" {print $ix["run_id"]}
  ' fastcat_stats/per-file-runids.tsv | sort | uniq > fastcat_stats/run_ids
  # get unique basecall models
  awk -F '\t' '
      NR==1 {for (i=1; i<=NF; i++) {ix[$i] = i}}
      # only print basecall model if present
      NR>1 && $ix["basecaller"] != "" {print $ix["basecaller"]}
  ' fastcat_stats/per-file-basecallers.tsv | sort | uniq > fastcat_stats/basecallers

Command exit status:
  1

Command output:
  (empty)

Command error:
  Error: unknown command "/xx/yyy/user/nextflow" for "apptainer"

  Error for command "apptainer": unknown flag: --no-home

  Options for apptainer command:

        --build-config    use configuration needed for building containers
    -c, --config string   specify a configuration file (for root or
                          unprivileged installation only) (default
                          "/cm/local/apps/apptainer/var/etc/apptainer/apptainer.conf")
    -d, --debug           print debugging information (highest verbosity)
    -h, --help            help for apptainer
        --nocolor         print without color output (default False)
    -q, --quiet           suppress normal output
    -s, --silent          only print errors
    -v, --verbose         print additional information
        --version         version for apptainer

  Run 'apptainer --help' for more detailed usage information.

Work dir:
  /xx/yyy/user/nextflow/work/dc/192083131afab55c0747651aac97be

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

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