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nextflow run nf-core/pathogensurveillance -r dev -profile singularity --input pathogen_manifest.csv --outdir pathogen_resultsTerminal Output:Execution cancelled -- Finishing pending tasks before exit-[nf-core/plantpathsurveil] Pipeline completed with errors-ERROR ~ Error executing process > 'NFCORE_PATHOGENSURVEILLANCE:PATHOGENSURVEILLANCE:INPUT_CHECK:SAMPLESHEET_CHECK (pathogen_manifest.csv)'Caused by: Process `NFCORE_PATHOGENSURVEILLANCE:PATHOGENSURVEILLANCE:INPUT_CHECK:SAMPLESHEET_CHECK (pathogen_manifest.csv)` terminated with an error exit status (1)Command executed: check_samplesheet.py \ pathogen_manifest.csv \ samplesheet.valid.csv cat <<-END_VERSIONS > versions.yml "NFCORE_PATHOGENSURVEILLANCE:PATHOGENSURVEILLANCE:INPUT_CHECK:SAMPLESHEET_CHECK": python: $(python --version | sed 's/Python //g') END_VERSIONSCommand exit status: 1Command output: (empty)Command error: INFO: Converting SIF file to temporary sandbox... WARNING: Skipping mount /home/elysebarker/miniconda3/envs/nextflow/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [CRITICAL] The given sample sheet does not appear to contain a header. INFO: Cleaning up image...Work dir: /hdd/2/elyse/microbiome/Sweden_MSU_metagenomics_shotgun/20240209_DNASeq_PE150/work/d6/a0cdf03190be8bfe860c27bc6d4ebbTip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` -- Check '.nextflow.log' file for details
Relevant files
No response
System information
I am using nextflow version 23.10.1 on linux.
nf-core/plantpathsurveil v1.0dev
The text was updated successfully, but these errors were encountered:
This changes often and may not work correctly, but it is much more developed than the version here. If you would like to try out the pipeline I highly recommend using this fork for the near future. Once we have a first release, development will transition to the main nf-core repository (this repository).
For now, where you see nf-core in the instructions, substitute grunwaldlab. Also check the README there for information on the input format. If you still get errors, feel free to let us know here.
Description of the bug
The error is saying I don't have a header in my csv file but I have the exact header as the tutorial.
sample,fastq_1,fastq_2 6_13_22,/hdd/2/elyse/microbiome/Sweden_MSU_metagenomics_shotgun/20240209_DNASeq_PE150/6_13_22_S36_L003_R1_001.fastq.gz,/hdd/2/elyse/microbiome/Sweden_MSU_metagenomics_shotgun/20240209_DNASeq_PE150/6_13_22_S36_L003_R2_001.fastq.gz 6_14_22,/hdd/2/elyse/microbiome/Sweden_MSU_metagenomics_shotgun/20240209_DNASeq_PE150/6_14_22_S37_L003_R1_001.fastq.gz,/hdd/2/elyse/microbiome/Sweden_MSU_metagenomics_shotgun/20240209_DNASeq_PE150/6_14_22_S37_L003_R2_001.fastq.gz
Command used and terminal output
Relevant files
No response
System information
I am using nextflow version 23.10.1 on linux.
nf-core/plantpathsurveil v1.0dev
The text was updated successfully, but these errors were encountered: