Closed jilldv closed 1 year ago
This is a critical issue. Could you try:
conda activate <conda env mentioned in first line>
mamba install python=3.8
comda deactivate
Try rerun atlas.
I just tried the commands above and started atlas again but unfortunately it gives the same error message.
Can you give me the content of the file : ' ../atlas_databases/condaenvs/f077e509b9873bc1010104c7314c8556.yaml'
We need to raise an error on snakemake repo. Maybe I have tome tomorrow..
And just to be shure can you run:
conda list python -p ../atlas_databases/conda_envs/f077e509b9873bc1010104c7314c8556_
`
I raised the issue at the snakemake repo.
Maybe what you can do is to install the snakemake-wrapper-utils
in the atlas env. This should be a hack.
Any others experiencing the problem?
Thank you for the fast response. The content from the file ' ../atlas_databases/condaenvs/f077e509b9873bc1010104c7314c8556.yaml' channels:
And the output from conda list python -p ../atlas_databases/conda_envs/f077e509b9873bc1010104c7314c8556_
# packages in environment at /home/jill/atlas_databases/conda_envs/f077e509b9873bc1010104c7314c8556_:
#
# Name Version Build Channel
python 3.8.16 he550d4f_1_cpython conda-forge
Maybe what you can do is to install the
snakemake-wrapper-utils
in the atlas env. This should be a hack.
I install this also with conda or not?
Everything looks as it should be. Yes, you can try to install snakemake-wrapper-utils with conda/mamba in the atlas env.
Can you tell me and on https://github.com/snakemake/snakemake/issues/2222 which version of snakemake you are using.
Maybe updating it to 7.25 could help.
The snakemake version I am using is 7.25.0
After installing snakemake-wrapper-utils the pipeline continued. However now I get an error running DAStool. This is the error message:
rule run_das_tool:
input: sample2/binning/DASTool/metabat.scaffolds2bin, sample2/binning/DASTool/maxbin.scaffolds2bin, sample2/sample2_contigs.fasta, sample2/annotation/predicted_genes/sample2.faa
output: sample2/binning/DASTool/sample2_DASTool_summary.tsv, sample2/binning/DASTool/sample2_allBins.eval, sample2/binning/DASTool/cluster_attribution.tsv
log: sample2/logs/binning/DASTool.log
jobid: 30
reason: Missing output files: sample2/binning/DASTool/cluster_attribution.tsv
wildcards: sample=sample2
threads: 2
resources: tmpdir=/tmp, mem=10, time_min=300, mem_mb=60000, mem_mib=57221, runtime=18000
Activating conda environment: ../atlas_databases/conda_envs/edb12c7f1add802bb49be03c8f52f012_
[Tue Apr 18 16:21:04 2023]
Error in rule run_das_tool:
jobid: 30
input: sample2/binning/DASTool/metabat.scaffolds2bin, sample2/binning/DASTool/maxbin.scaffolds2bin, sample2/sample2_contigs.fasta, sample2/annotation/predicted_genes/sample2.faa
output: sample2/binning/DASTool/sample2_DASTool_summary.tsv, sample2/binning/DASTool/sample2_allBins.eval, sample2/binning/DASTool/cluster_attribution.tsv
log: sample2/logs/binning/DASTool.log (check log file(s) for error details)
conda-env: /home/jill/atlas_databases/conda_envs/edb12c7f1add802bb49be03c8f52f012_
shell:
DAS_Tool --outputbasename sample2/binning/DASTool/sample2 --bins sample2/binning/DASTool/metabat.scaffolds2bin,sample2/binning/DASTool/maxbin.scaffolds2bin --labels metabat,maxbin --contigs sample2/sample2_contigs.fasta --search_engine diamond --proteins sample2/annotation/predicted_genes/sample2.faa --write_bin_evals --megabin_penalty 0.5 --duplicate_penalty 0.6 --threads 2 --debug --score_threshold 0.5 &> sample2/logs/binning/DASTool.log ; mv sample2/binning/DASTool/sample2_DASTool_contig2bin.tsv sample2/binning/DASTool/cluster_attribution.tsv &>> sample2/logs/binning/DASTool.log
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
The content from the log file 'sample2/logs/binning/DASTool.log': Error in library(docopt, warn.conflicts = F, quietly = T) : there is no package called ‘docopt’ Calls: suppressMessages -> withCallingHandlers Execution halted
I tried installing docopt in the ../atlas_databases/condaenvs/edb12c7f1add802bb49be03c8f52f012 environment but I keep getting the same error message.
So there is an error in the r-package docopt ?
could you send me the output of the conda list docopt -p ...path to conda env
What about using another binner as final_binner
in the config file. e.g. vamb if you have less than 100 samples.
Thank you for reporting
This is the output
(atlas) jill@WE11sv03:~/atlas_test$ conda list docopt -p ../atlas_databases/conda_envs/edb12c7f1add802bb49be03c8f52f012_
# packages in environment at /home/jill/atlas_databases/conda_envs/edb12c7f1add802bb49be03c8f52f012_:
#
# Name Version Build Channel
docopt 0.6.2 py_1 conda-forge
r-docopt 0.7.1 r42hc72bb7e_2 conda-forge
I can use another binner I think. Do these other binners also do bin refinement or is this not really necessary for running the genome workflow?
Sorry for all the questions and error messages.
Other binners don't use bin refinement but finally vamb gives better results.
It seems to be ab error with this r package.
We had someti es the problem with other R version in the path that took precedence ocer the R version of the conda env from snakemake.
Could you please activate the conda env of the DAStool and print out the $PATH varable.
This is the $PATH I get:
/home/jill/atlas_databases/condaenvs/edb12c7f1add802bb49be03c8f52f012/share/rubygems/bin:/home/jill/bin:/home/jill/.local/bin:/usr/bin:/home/bioadmin/Downloads/FastQC-0.11.9/fastqc:/home/jill/bin:/home/jill/.local/bin:/usr/bin:/home/bioadmin/Downloads/FastQC-0.11.9/fastqc:/home/jill/atlas_databases/condaenvs/edb12c7f1add802bb49be03c8f52f012/bin:/home/bioadmin/miniconda3/condabin:/usr/local/ncbi/sra-tools/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/bin/usearch:$HOME/.local/bin:~/.cache:/usr/local/bin/spades/SPAdes-3.11.1-Linux/bin:/snap/bin:/home/jill/bin:/usr/lib/jvm/java-8-openjdk-amd64/bin/java/bin:/home/bioadmin/Downloads/squeezeMeta/SqueezeMeta-1.0.0/scripts:/home/mbogorad/RNAQCchain/RNA-QC-Chain/bin:/home/jill/bin:/usr/lib/jvm/java-8-openjdk-amd64/bin/java/bin:/home/bioadmin/Downloads/squeezeMeta/SqueezeMeta-1.0.0/scripts:/home/mbogorad/RNAQCchain/RNA-QC-Chain/bin
It is possible that there is another R version in your path.
Could you try:
conda activate /home/jill/atlas_databases/conda_envs/edb12c7f1add802bb49be03c8f52f012_
which R
and if it is not the R from the conda env. I suggest you to simplyfy the path.
Maybe you need to do this itteratively.
Sorry for my late response, some work came in between so I could only now come back to this. Indeed the wrong R version was used. I adjusted the path so the correct version was used and I was finally able to finish the pipeline. Thank you for all the help!
align_reads_to_final_contigs
Here is the relevant log output:
Atlas version 2.15.0
Additional context I installed atlas using conda, following the documentation. Now I am trying to run the pipeline using the test data also provided in the documentation. But I encountered this error. When installing atlas into a conda environment I specified python version 3.8, but it seems there is some kind of mixup between versions. When I run
conda list python -f
in the activated atlas environment I get the following:I am not sure what to do or what went wrong exactly.