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stenglein-lab / taxonomy_pipeline

A nextflow pipeline to taxonomically assess the sequences in an NGS dataset, with a focus on identifying and characterizing virus sequences
MIT License
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Issue with conda environment #15

Open james-weger opened 1 year ago

james-weger commented 1 year ago

Hi Mark.

I'm having an issue where it doesn't appear to be installing the conda environment. I'm in my base conda env, and I'm running the following command:

nextflow run main.nf -resume -profile conda --host_map_file /work/cascades/weger/2022_3_analysis/input/host_mapping.txt --nt_blast_db /work/cascades/weger/databases/nt --nt_diamond_db /work/cascades/weger/databases/nr --fastq_pattern _R[12].fastq

I'm getting this error: Error executing process > 'initial_qc (1)'

Caused by: Process initial_qc (1) terminated with an error exit status (127)

Command executed:

mkdir -p /work/cascades/weger/2022_3_analysis/results/initial_fastqc/ fastqc -o /work/cascades/weger/2022_3_analysis/results/initial_fastqc/ 8-3_R1.fastq.gz 8-3_R2.fastq.gz

Command exit status: 127

Command output: (empty)

Command error: .command.sh: line 3: fastqc: command not found

Work dir: /work/cascades/weger/2022_3_analysis/work/a5/5c6bc5aaf0f01929f7577bc7a53fa4

Do you have any thoughts on what I'm doing wrong?

james-weger commented 1 year ago

Update: I also tried to run it with singularity. Just to show which version of singularity and nextflow I have:

(base) [weger@calogin1 2022_3_analysis]$ singularity --version singularity version 3.8.6

(base) [weger@calogin1 2022_3_analysis]$ nextflow -version

  N E X T F L O W
  version 22.10.4 build 5836
  created 09-12-2022 09:58 UTC (04:58 EDT)
  cite doi:10.1038/nbt.3820
  http://nextflow.io

I then run the following command: nextflow run main.nf -resume -profile singularity,local --host_map_file /work/cascades/weger/2022_3_analysis/input/host_mapping.txt --nt_blast_db /work/cascades/weger/databases/nt --nt_diamond_db /work/cascades/weger/databases/nr --fastq_pattern _R[12].fastq

This is the error message I get: Pulling Singularity image https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0 [cache /home/weger/singularity_cacheDir/depot.galaxyproject.org-singularity-fastqc-0.11.9--0.img] Error executing process > 'trim_adapters_and_low_quality (1)'

Caused by: Process trim_adapters_and_low_quality (1) terminated with an error exit status (255) Command executed:

cutadapt -a AGATCGGAAGAGC -g GCTCTTCCGATCT -a AGATGTGTATAAGAGACAG -g CTGTCTCTTATACACATCT -A AGATCGGAAGAGC -G GCTCTTCCGATCT -A AGATGTGTATAAGAGACAG -G CTGTCTCTTATACACATCT -q 30,30 --minimum-length 30 -u 0 -u -1 -U 0 -U -1 -o 8-3_R1_f.fastq -p 8-3_R2_f.fastq 8-3_R1.fastq.gz 8-3_R2.fastq.gz

Command exit status: 255

Command output: (empty)

Command error: INFO: Converting SIF file to temporary sandbox... FATAL: while extracting /home/weger/singularity_cacheDir/depot.galaxyproject.org-singularity-cutadapt-3.5--py39h38f01e4_0.img: root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace disabled : exit status 1

Work dir: /work/cascades/weger/2022_3_analysis/work/5c/27aac207e7c334d817a520d88b8cd9

Please let me know if you need more information.