Open spencer411 opened 2 years ago
Let me look into this, it's clearly not working
Can you tell me which version of python and Snakemake you're using?
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From: spencer411 @.> Sent: Tuesday, September 21, 2021 7:41:07 PM To: WatsonLab/MAGpy @.> Cc: Subscribed @.***> Subject: [WatsonLab/MAGpy] install issues (#39)
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Just trying to install and run this on our cluster. When I run the command: snakemake -rp -s MAGpy --cores 1 --use-conda test
I get the following error, but everything else seems to run fine:
scripts/add_tax.py ran with some errors: File "/network/rit/lab/andamlab/bin/MAGpy/scripts/add_tax.py", line 95 k = names[l] TabError: inconsistent use of tabs and spaces in indentation
Further more if I move to the next step and run: snakemake -rp -s MAGpy --cores 16 --use-conda setup
It finishes very quickly, and reviewing the log file it says:
The flag 'directory' used in rule all is only valid for outputs, not inputs. Building DAG of jobs... Nothing to be done.
Am I missing something here with the install?
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If I activate the magpy_install env and type "python --version" its says Python 3.9.7. Nevertheless if I type conda info, it says python version : 3.8.8.final.0.
Looking back at when I ran conda env create -f envs/install.yaml it says I installed snakemake-6.8.0
The series of code I ran based on the github site looked like this, just ensure I am doing things correctly:
git clone https://github.com/WatsonLab/MAGpy.git cd MAGpy conda env create -f envs/install.yaml conda activate magpy_install snakemake -rp -s MAGpy --cores 1 --use-conda test snakemake -rp -s MAGpy --cores 16 --use-conda setup
Note that I am using miniconda3
Thanks!
OK, latest commit should have solved most things
You need to run
rm -rf magpy_dbs
after running the tests, sorry about that
Having a new issue here when I run "snakemake -rp -s MAGpy --cores 16 --use-conda setup".
It run fine for a while and then I get:
Database sequences 219174961 Database letters 75271144009 Database hash c95ef6a1a2e26795e19cb50f839b44e7 Total time 2711s [Wed Oct 6 09:58:53 2021] Error in rule setup: jobid: 0 output: magpy_dbs conda-env: /network/rit/lab/andamlab/bin/MAGpy/.snakemake/conda/12db78cf454bed3ea850367e3b9143d7 shell:
mkdir -p magpy_dbs && cd magpy_dbs
wget -q ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz
diamond makedb --threads 4 --in uniprot_trembl.fasta.gz -d uniprot_trembl
rm uniprot_trembl.fasta.gz
# Sourmash
wget -O genbank-k21.lca.json.gz -q https://osf.io/d7rv8/download
wget -O genbank-k31.lca.json.gz -q https://osf.io/4f8n3/download
wget -O genbank-k51.lca.json.gz -q https://osf.io/nemkw/download
# Pfam
wget -q ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
wget -q ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.dat.gz
#wget -q ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/active_site.dat.gz
gunzip Pfam-A.hmm.gz Pfam-A.hmm.dat.gz #active_site.dat.gz
hmmpress Pfam-A.hmm
# get checkM data
mkdir checkm_data
cd checkm_data
wget -q https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
gunzip < checkm_data_2015_01_16.tar.gz | tar xvf -
cd ..
cd ..
echo '{"uniprot_sprot": "magpy_dbs/uniprot_trembl.dmnd","sourmash_gbk_k21": "magpy_dbs/genbank-k21.lca.json.gz","sourmash_gbk_k31": "magpy_dbs/genbank-k31.lca.json.gz","sourmash_gbk_k51": "magpy_dbs/genbank-k51.lca.json.gz","pfam_dir": "magpy_dbs","checkm_dataroot": "magpy_dbs/checkm_data"}' > config.json
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Removing output files of failed job setup since they might be corrupted: magpy_dbs Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /network/rit/lab/andamlab/bin/MAGpy/.snakemake/log/2021-10-06T090641.681886.snakemake.log
Ach that's annoying because it's going to delete everything and only one step went wrong.
I will try and split the steps and see what's happening
I also got an error, and tracked it down to the sourmash wget steps:
Resolving osf.io (osf.io)... 35.190.84.173
Connecting to osf.io (osf.io)|35.190.84.173|:443... connected.
ERROR: cannot verify osf.io's certificate, issued by ‘/C=US/O=Let's Encrypt/CN=R3’:
Issued certificate has expired.
To connect to osf.io insecurely, use `--no-check-certificate'.
You could try that, or wait until I test this thing...
I just pushed a new commit which splits up the steps, so shouldn't delete progress if just one of them fails
It all just ran fine for me :)
Just trying to install and run this on our cluster. When I run the command: snakemake -rp -s MAGpy --cores 1 --use-conda test
I get the following error, but everything else seems to run fine:
scripts/add_tax.py ran with some errors: File "/network/rit/lab/andamlab/bin/MAGpy/scripts/add_tax.py", line 95 k = names[l] TabError: inconsistent use of tabs and spaces in indentation
Further more if I move to the next step and run: snakemake -rp -s MAGpy --cores 16 --use-conda setup
It finishes very quickly, and reviewing the log file it says:
The flag 'directory' used in rule all is only valid for outputs, not inputs. Building DAG of jobs... Nothing to be done.
Am I missing something here with the install?