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

[gabyrech]

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