You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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 completecommand 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
The text was updated successfully, but these errors were encountered:
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.
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
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
The text was updated successfully, but these errors were encountered: