Open Syutenjyo opened 3 years ago
Dear Everyone,
I just have failed to run this program. /(ㄒoㄒ)/~~ The command I used is like this "nextflow run ../NanoCLUST-master/main.nf -profile test,conda"
'''
[nf-core/nanoclust] Pipeline completed with errors Error executing process > 'output_documentation'
Caused by: Process output_documentation terminated with an error exit status (1)
output_documentation
Command executed:
markdown_to_html.py 3pipeline_output.md -o results_description.html
Command exit status: 1
Command output: (empty)
Command error: .command.sh: line 2: /home/wuxiaoyun/ztz/20210623/NanoCLUST-master/bin/markdown_to_html.py: Permission denied
Work dir: /home/wuxiaoyun/ztz/20210623/result/work/fe/10ff2b21a20e21eeefe3622fd92c80
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
bash .command.run
''' '''
[- ] process > QC - [- ] process > fastqc - executor > local (1) executor > local (1) [51/737004] process > QC (1) [100%] 1 of 1 ✔ executor > local (2) [51/737004] process > QC (1) [100%] 1 of 1 ✔ executor > local (2) [51/737004] process > QC (1) [100%] 1 of 1 ✔ executor > local (2) [51/737004] process > QC (1) [100%] 1 of 1 ✔ executor > local (2) [51/737004] process > QC (1) [100%] 1 of 1 ✔ executor > local (2) [51/737004] process > QC (1) [100%] 1 of 1 ✔ executor > local (2) [51/737004] process > QC (1) [100%] 1 of 1 ✔ [- ] process > fastqc - [- ] process > kmer_freqs - [- ] process > read_clustering - [- ] process > split_by_cluster - [- ] process > read_correction - [- ] process > draft_selection - [- ] process > racon_pass - [- ] process > medaka_pass - [- ] process > consensus_classification - [- ] process > join_results - [- ] process > get_abundances - [- ] process > plot_abundances - [fe/10ff2b] process > output_documentation [100%] 1 of 1, failed: 1 ✘ Creating Conda env: /home/wuxiaoyun/ztz/20210623/NanoCLUST-master/conda_envs/kmer_freqs/environment.yml [cache /home/wuxiaoyun/ztz/20210623/result/work/conda/kmer_freq-999fbd7473cd6106e662a85d832c592d] Creating Conda env: /home/wuxiaoyun/ztz/20210623/NanoCLUST-master/conda_envs/fastqc/environment.yml [cache /home/wuxiaoyun/ztz/20210623/result/work/conda/fastqc_multiqc-fddb8d2dd7b722375e53387e3daf8470] Execution cancelled -- Finishing pending tasks before exit
I am new in bioinformatics.can you help me to solve this problem? Thank you very much! (^_^)
Dear Everyone,
I just have failed to run this program. /(ㄒoㄒ)/~~ The command I used is like this "nextflow run ../NanoCLUST-master/main.nf -profile test,conda"
'''
[nf-core/nanoclust] Pipeline completed with errors Error executing process > 'output_documentation'
Caused by: Process
output_documentation
terminated with an error exit status (1)Command executed:
markdown_to_html.py 3pipeline_output.md -o results_description.html
Command exit status: 1
Command output: (empty)
Command error: .command.sh: line 2: /home/wuxiaoyun/ztz/20210623/NanoCLUST-master/bin/markdown_to_html.py: Permission denied
Work dir: /home/wuxiaoyun/ztz/20210623/result/work/fe/10ff2b21a20e21eeefe3622fd92c80
Tip: you can replicate the issue by changing to the process work dir and entering the command
bash .command.run
''' '''
[- ] process > QC - [- ] process > fastqc - executor > local (1) executor > local (1) [51/737004] process > QC (1) [100%] 1 of 1 ✔ executor > local (2) [51/737004] process > QC (1) [100%] 1 of 1 ✔ executor > local (2) [51/737004] process > QC (1) [100%] 1 of 1 ✔ executor > local (2) [51/737004] process > QC (1) [100%] 1 of 1 ✔ executor > local (2) [51/737004] process > QC (1) [100%] 1 of 1 ✔ executor > local (2) [51/737004] process > QC (1) [100%] 1 of 1 ✔ executor > local (2) [51/737004] process > QC (1) [100%] 1 of 1 ✔ [- ] process > fastqc - [- ] process > kmer_freqs - [- ] process > read_clustering - [- ] process > split_by_cluster - [- ] process > read_correction - [- ] process > draft_selection - [- ] process > racon_pass - [- ] process > medaka_pass - [- ] process > consensus_classification - [- ] process > join_results - [- ] process > get_abundances - [- ] process > plot_abundances - [fe/10ff2b] process > output_documentation [100%] 1 of 1, failed: 1 ✘ Creating Conda env: /home/wuxiaoyun/ztz/20210623/NanoCLUST-master/conda_envs/kmer_freqs/environment.yml [cache /home/wuxiaoyun/ztz/20210623/result/work/conda/kmer_freq-999fbd7473cd6106e662a85d832c592d] Creating Conda env: /home/wuxiaoyun/ztz/20210623/NanoCLUST-master/conda_envs/fastqc/environment.yml [cache /home/wuxiaoyun/ztz/20210623/result/work/conda/fastqc_multiqc-fddb8d2dd7b722375e53387e3daf8470] Execution cancelled -- Finishing pending tasks before exit
'''
I am new in bioinformatics.can you help me to solve this problem? Thank you very much! (^_^)