General info
I've been trying to run piranha on linux (inside an HPC) but am unable to run it on wg analysis mode. When I run on VP1 mode (default) it runs just fine, but whenever I try the wg mode I get an error saying the snakefile piranha_wg.smk couldn't be found (more details below).
I'm running piranha version 1.2.5. I've tried running it from a conda environment and a singularity container. Given the permissions set by the HPC I'm working on, I'm unable to use Docker, and when I try installing it from source, I get several incompatibility errors (same as reported on issue #223).
Running from a Conda environment
The conda environment was built with the following commands:
Error: cannot find Snakefile at /scicomp/home-pure/xwe3/.conda/envs/piranha-polio/lib/python3.8/site-packages/piranha/scripts/piranha_wg.smk
Check installation or specify another analysis mode
When I check the folder /scicomp/home-pure/xwe3/.conda/envs/piranha-polio/lib/python3.8/site-packages/piranha/scripts/ the snakefile piranha_wg.smk is not there:
~/xwe3/workdir/PolioONTbenchmark/piranha/JamesSamples$ ll /scicomp/home-pure/xwe3/.conda/envs/piranha-polio/lib/python3.8/site-packages/piranha/scripts/
total 39
-rw-------. 2 xwe3 users 0 Jun 19 12:21 __init__.py
drwx--S---. 2 xwe3 users 0 Jun 20 13:18 __pycache__
-rw-------. 2 xwe3 users 7206 Jun 19 12:21 piranha_consensus.smk
-rw-------. 2 xwe3 users 6611 Jun 19 12:21 piranha_curate.smk
-rw-------. 2 xwe3 users 6802 Jun 19 12:21 piranha_haplotype.smk
-rw-------. 2 xwe3 users 2488 Jun 19 12:21 piranha_phylo.smk
-rw-------. 2 xwe3 users 4575 Jun 19 12:21 piranha_preprocessing.smk
-rw-------. 2 xwe3 users 2504 Jun 19 12:21 piranha_variation.smk
-rw-------. 2 xwe3 users 8509 Jun 19 12:21 piranha_vp1.smk
I've tried downloading the piranha_wg.smk file from the github repo into this folder (not ideal, but I thought it was worth trying before opening an issue) and run the aforementioned command again, and I get the following error after the analysis runs for a little bit:
Error in rule gather_consensus_sequences:
jobid: 0
input: /scicomp/scratch/xwe3/workdir/PolioONTbenchmark/piranha/JamesSamples/JamesSamplesVP1_62724_wg/sample_composition.csv
output: /scicomp/scratch/xwe3/workdir/PolioONTbenchmark/piranha/JamesSamples/JamesSamplesVP1_62724_wg/published_data/vp1_sequences.fasta
RuleException:
TypeError in file /scicomp/home-pure/xwe3/.conda/envs/piranha-polio/lib/python3.8/site-packages/piranha/scripts/piranha_wg.smk, line 98:
gather_fasta_files() missing 2 required positional arguments: 'publish_dir' and 'config'
File "/scicomp/home-pure/xwe3/.conda/envs/piranha-polio/lib/python3.8/site-packages/piranha/scripts/piranha_wg.smk", line 98, in __rule_gather_consensus_sequences
File "/scicomp/home-pure/xwe3/.conda/envs/piranha-polio/lib/python3.8/concurrent/futures/thread.py", line 57, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-06-28T092052.455429.snakemake.log
The complete log file is not very informative (see below):
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job count
-------------------------- -------
all 1
gather_consensus_sequences 1
total 2
Select jobs to execute...
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-06-28T092052.455429.snakemake.log
I thought this could be a problem with the conda environment I created, so I tried running it from a singularity container (see below).
Running from Singularity container
To run the pipeline on a singularity container, I downloaded piranha's image from Galaxy and ran it with the following command:
Almost immediately, I get the same error as with the conda environment:
Error: cannot find Snakefile at /usr/local/lib/python3.9/site-packages/piranha/scripts/piranha_wg.smk
Check installation or specify another analysis mode
When I check the content of that folder, the piranha_wg.smk is not there. Next, I tried going into the singularity container with singularity shell ~/singularityIMG/piranha-polio%3A1.2.5--pyhdfd78af_0, and when I check the contents of the container the following options show up (still no piranha_wg.smk):
Concluding remarks
I've had the HPC support team to replicate the same errors and I was able to replicate the errors on my local computer, suggesting this is not an issue with the environments I'm using. I've also tried the aforementioned on a different version of piranha (1.2.2) with the same results.
Is it possible the piranha_wg.smk snakefile is not included in the singularity container available on Galaxy and in the conda install files? Again, I can run the analysis on VP1 mode just fine both on singularity and conda.
Any help would be greatly appreciated!
Thanks,
Eduardo
General info I've been trying to run piranha on linux (inside an HPC) but am unable to run it on
wganalysis mode. When I run onVP1mode (default) it runs just fine, but whenever I try thewgmode I get an error saying the snakefilepiranha_wg.smkcouldn't be found (more details below).I'm running piranha version 1.2.5. I've tried running it from a conda environment and a singularity container. Given the permissions set by the HPC I'm working on, I'm unable to use Docker, and when I try installing it from source, I get several incompatibility errors (same as reported on issue #223).
Running from a Conda environment The conda environment was built with the following commands:
After successfully installing piranha, I run the following commands to activate the environment and run the pipeline:
Instantly, I get the following error:
When I check the folder
/scicomp/home-pure/xwe3/.conda/envs/piranha-polio/lib/python3.8/site-packages/piranha/scripts/the snakefilepiranha_wg.smkis not there:I've tried downloading the
piranha_wg.smkfile from the github repo into this folder (not ideal, but I thought it was worth trying before opening an issue) and run the aforementioned command again, and I get the following error after the analysis runs for a little bit:The complete log file is not very informative (see below):
I thought this could be a problem with the conda environment I created, so I tried running it from a singularity container (see below).
Running from Singularity container To run the pipeline on a singularity container, I downloaded piranha's image from Galaxy and ran it with the following command:
Almost immediately, I get the same error as with the conda environment:
When I check the content of that folder, the piranha_wg.smk is not there. Next, I tried going into the singularity container with
singularity shell ~/singularityIMG/piranha-polio%3A1.2.5--pyhdfd78af_0, and when I check the contents of the container the following options show up (still no piranha_wg.smk):Concluding remarks I've had the HPC support team to replicate the same errors and I was able to replicate the errors on my local computer, suggesting this is not an issue with the environments I'm using. I've also tried the aforementioned on a different version of piranha (1.2.2) with the same results. Is it possible the piranha_wg.smk snakefile is not included in the singularity container available on Galaxy and in the conda install files? Again, I can run the analysis on VP1 mode just fine both on singularity and conda.
Any help would be greatly appreciated! Thanks, Eduardo