nf-core
The issue is about the install
-[nf-core/chipseq] Pipeline completed with errors- i'm install this pipline in our lab server.but it have a problem. i guess that it's because the network. I don't know if there is a solution
(/media/_Extend2020/xxy/worke_chipseq) [xxy@localhost worke_chipseq]$ nextflow run nf-core/chipseq -profile test,conda
N E X T F L O W ~ version 22.04.5
Launching https://github.com/nf-core/chipseq [stoic_baekeland] DSL1 - revision: 6924b66942 [master]
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nf-core/chipseq v1.2.2
Run Name : stoic_baekeland Data Type : Paired-End Design File : https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/design.csv Genome : Not supplied Fasta File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa GTF File : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf MACS2 Genome Size : 1.2E+7 Min Consensus Reps : 1 MACS2 Narrow Peaks : No MACS2 Broad Cutoff : 0.1 Trim R1 : 0 bp Trim R2 : 0 bp Trim 3' R1 : 0 bp Trim 3' R2 : 0 bp NextSeq Trim : 0 bp Fingerprint Bins : 100 Save Genome Index : No Max Resources : 6 GB memory, 2 cpus, 12h time per job Output Dir : ./results Launch Dir : /media/_Extend2020/xxy/worke_chipseq Working Dir : /media/_Extend2020/xxy/worke_chipseq/work Script Dir : /home/xxy/.nextflow/assets/nf-core/chipseq User : xxy Config Profile : test,conda Config Description : Minimal test dataset to check pipeline function
[- ] process > CHECK_DESIGN - [- ] process > BWA_INDEX - [- ] process > MAKE_GENE_BED - [- ] process > MAKE_GENOME_FILTER - [- ] process > FASTQC - [- ] process > CHECK_DESIGN - [- ] process > BWA_INDEX - [- ] process > MAKE_GENE_BED - [- ] process > MAKE_GENOME_FILTER - [- ] process > FASTQC - [- ] process > CHECK_DESIGN - [- ] process > BWA_INDEX - [- ] process > MAKE_GENE_BED - [- ] process > MAKE_GENOME_FILTER - [- ] process > FASTQC - [- ] process > CHECK_DESIGN - [- ] process > BWA_INDEX - [- ] process > MAKE_GENE_BED - [- ] process > MAKE_GENOME_FILTER - [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > CHECK_DESIGN - [- ] process > BWA_INDEX - [- ] process > MAKE_GENE_BED - [- ] process > MAKE_GENOME_FILTER - [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > CHECK_DESIGN - [- ] process > BWA_INDEX - [- ] process > MAKE_GENE_BED - [- ] process > MAKE_GENOME_FILTER - [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_BAM - [- ] process > MERGED_BAM_FILTER - [- ] process > MERGED_BAM_REMOVE_ORPHAN - [- ] process > PRESEQ - [- ] process > PICARD_METRICS - [- ] process > BIGWIG - [- ] process > PLOTPROFILE - [- ] process > PHANTOMPEAKQUALTOOLS - [- ] process > CHECK_DESIGN - [- ] process > BWA_INDEX - [- ] process > MAKE_GENE_BED - [- ] process > MAKE_GENOME_FILTER - [- ] process > FASTQC - [- ] process > TRIMGALORE - [- ] process > BWA_MEM - [- ] process > SORT_BAM - [- ] process > MERGED_BAM - [- ] process > MERGED_BAM_FILTER - [- ] process > MERGED_BAM_REMOVE_ORPHAN - [- ] process > PRESEQ - [- ] process > PICARD_METRICS - [- ] process > BIGWIG - [- ] process > PLOTPROFILE - [- ] process > PHANTOMPEAKQUALTOOLS - [- ] process > PLOTFINGERPRINT - [- ] process > MACS2 - [- ] process > MACS2_ANNOTATE - [- ] process > MACS2_QC - [- ] process > CONSENSUS_PEAKS - [- ] process > CONSENSUS_PEAKS_ANNOTATE - [- ] process > CONSENSUS_PEAKS_COUNTS - [- ] process > CONSENSUS_PEAKS_DESEQ2 - [- ] process > IGV - [- ] process > get_software_versions - [- ] process > MULTIQC - [- ] process > output_documentation - Error executing process > 'output_documentation'
Caused by: Failed to create Conda environment command: conda env create --prefix /media/_Extend2020/xxy/worke_chipseq/work/conda/nf-core-chipseq-1.2.2-dcaaa83b75a9ed5b2ac0d32a507f2d8e --file /home/xxy/.nextflow/assets/nf-core/chipseq/environment.yml status : 143 message:（Nothing）
This seems to be a problem will resolving the conda environment of the pipeline which was quite huge in version 1.2.0 of the pipeline. The good news is that we just released version 2.0.0 of the pipeline yesterday so may be worth giving a try. Anyway, if possible we recommend using Docker or Singularity.
