UpalabdhaD commented 1 year ago

Dear Robert, Thanks for the wonderful bactopia. I have thoroughly enjoyed the bactopia paper and found it suitable for my analysis. However, I didn't have much luck running it successfully. Would be great to have your help.

1. my shell script

`

Source conda shell

source $HOME/anaconda3/etc/profile.d/conda.sh

include proxy for downloading data

export http_proxy='http://username:passwd@ip-address-univ/' export https_proxy='http://username:passwd@ip-address-univ/' export ftp_proxy='http://username:passwd@ip-address-univ/'

#########################

Directory paths

######################### Bactopia_top="$HOME/Documents/01_Work_nucleix/02_Prj_Rso_WGS/Bactopia_Rso" BaDs="$HOME/Documents/01_Work_nucleix/02_Prj_Rso_WGS/Bactopia_Rso/02_Ralstonia_dataset" Ralstonia_seq="$HOME/Documents/01_Work_nucleix/02_Prj_Rso_WGS/Bactopia_Rso/05_Ralstonia_sequences"

activate conda enviornment

conda activate bactopia

#########################

Build Datasets

#########################

time bactopia \ datasets \ --species "Ralstonia solanacearum" \ --include_genus \ --cpus 8 \ --outdir $BaDs

#####################################################

Query ENA for all Ralstonia Sequence projects

#####################################################

taxonomy id for R.solanacerum is 305

time bactopia \ search \ 305 \ --prefix Ralstonia_ENA \ --outdir $Bactopia_top/05_Ralstonia_sequences

##################################################

Run bactopia command

################################################ time bactopia \ --accessions $Ralstonia_seq/Ralstonia_ENA-accessions.txt \ --use_ena \ --datasets $BaDs/ \ --species "Ralstonia solanacearum" \ --genome_size 5500000 \ --coverage 50 \ --cleanup_workdir \ --outdir $Bactopia_top/trial_10

conda deactivate `

Bash Output:

bash bactopia_rso.sh 2022-11-21 15:56:27:root:INFO - Checking if environment pre-builds are needed, use --verbose to see full details. 2022-11-21 15:56:27:root:INFO - Found Conda environments in /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/conda/envs, if a complete rebuild is needed please use --force_rebuild N E X T F L O W ~ version 22.10.1 Launching /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/main.nf [desperate_bassi] DSL2 - revision: 145bb11899

| | _ | | __ (_)
| ' \ / ` |/ | / | ' | |/ ` |
| |) | (| | (| || () | |) | | (| |
|./ _,|_|__/| ./||_,| |_|
bactopia v2.1.1 Bactopia is a flexible pipeline for complete analysis of bacterial genomes.

Core Nextflow options runName : desperate_bassi launchDir : /home/upalabdha/Documents/01_Work_nucleix/02_Prj_Rso_WGS/Bactopia_Rso/03_script workDir : /home/upalabdha/Documents/01_Work_nucleix/02_Prj_Rso_WGS/Bactopia_Rso/03_script/work projectDir : /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x userName : upalabdha profile : standard configFiles : /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/nextflow.config

Required Parameters accessions : /home/upalabdha/Documents/01_Work_nucleix/02_Prj_Rso_WGS/Bactopia_Rso/05_Ralstonia_sequences/Ralstonia_ENA-accessions.txt

Dataset Parameters datasets : /home/upalabdha/Documents/01_Work_nucleix/02_Prj_Rso_WGS/Bactopia_Rso/02_Ralstonia_dataset/ species : Ralstonia solanacearum coverage : 50 genome_size : 5500000

Gather Samples Parameters use_ena : true

Optional Parameters outdir : /home/upalabdha/Documents/01_Work_nucleix/02_Prj_Rso_WGS/Bactopia_Rso/trial_10

Nextflow Configuration Parameters cleanup_workdir : true

Nextflow Profile Parameters condadir : /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/conda/envs registry : quay singularity_cache: /home/upalabdha/.bactopia/singularity

!! Only displaying parameters that differ from the pipeline defaults !!

If you use bactopia for your analysis please cite:

Bactopia https://doi.org/10.1128/mSystems.00190-20
The nf-core framework https://doi.org/10.1038/s41587-020-0439-x
Software dependencies https://bactopia.github.io/acknowledgements/

WARN: WARN: Conda Disclaimer WARN: WARN: If you have access to Docker or Singularity, please consider WARN: running Bactopia using containers. The containers are less WARN: susceptible to Conda environment related issues (e.g. version WARN: conflicts) and errors caused by creation of conda environments WARN: in parallel (use '--max_cpus 1' to over come this error). WARN: WARN: To use containers, you can use the profile parameter WARN: Docker: -profile docker WARN: Singularity: -profile singularity WARN:

Unable to read script: '/home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/./workflows/../modules/local/bactopia/assemble_genome/main.nf' -- cause: Can't find a matching module file for include: ../../../lib/nf/functions

real 0m6.569s user 0m39.539s sys 0m1.369s

If you want anything else for help please let me know. Currently I am using a i7 cpu 16 thread desktop computer with 64Gb RAM configured with Debian, Conda version 22.9.0

Thanks in advance, Upalabdha

rpetit3 commented 1 year ago

Hi @UpalabdhaD

Let's see if you can get this going for you! What is the output of:

ls -lh /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/./workflows/../modules/local/bactopia/assemble_genome/../../../lib/nf/

UpalabdhaD commented 1 year ago

hi @rpetit3 Thanks for your quick response. here is output of ls -lh ❯ ls -lh /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/./workflows/../modules/local/bactopia/assemble_genome/../../../lib/nf/ ls: cannot access '/home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/./workflows/../modules/local/bactopia/assemble_genome/../../../lib/nf/': No such file or directory

rpetit3 commented 1 year ago

OK, what about here? ls -lh /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/

UpalabdhaD commented 1 year ago

Here you go @rpetit3

❯ ls -lh /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/
total 48K
drwxr-xr-x 5 upalabdha upalabdha 4.0K Nov 19 19:55 bin
drwxr-xr-x 6 upalabdha upalabdha 4.0K Nov 20 13:37 conda
drwxr-xr-x 5 upalabdha upalabdha 4.0K Nov 19 19:55 conf
drwxr-xr-x 2 upalabdha upalabdha 4.0K Nov 19 19:55 data
drwxr-xr-x 3 upalabdha upalabdha 4.0K Nov 19 19:55 lib
-rw-rw-r-- 2 upalabdha upalabdha 1.3K Nov  8 09:45 main.nf
drwxr-xr-x 4 upalabdha upalabdha 4.0K Nov 19 19:55 modules
-rw-rw-r-- 2 upalabdha upalabdha 5.4K Nov  8 09:45 nextflow.config
drwxr-xr-x 3 upalabdha upalabdha 4.0K Nov 19 19:55 subworkflows
drwxr-xr-x 5 upalabdha upalabdha 4.0K Nov 19 19:55 tests
drwxr-xr-x 2 upalabdha upalabdha 4.0K Nov 19 19:55 workflows

rpetit3 commented 1 year ago

OK,

ls -lh /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/lib/nf

ls -lh /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/./workflows/../modules/local/bactopia/assemble_genome

UpalabdhaD commented 1 year ago

❯ ls -lh /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/lib/nf
total 40K
-rw-rw-r-- 2 upalabdha upalabdha  20K Nov  8 09:45 bactopia.nf
-rw-rw-r-- 2 upalabdha upalabdha 7.5K Nov  8 09:45 bactopia_tools.nf
-rw-rw-r-- 2 upalabdha upalabdha 9.0K Nov  8 09:45 functions.nf

❯ ls -lh /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/./workflows/../modules/local/bactopia/assemble_genome
total 72K
-rw-rw-r-- 2 upalabdha upalabdha  594 Nov  8 09:45 README.md
-rw-rw-r-- 2 upalabdha upalabdha  12K Nov  8 09:45 main.nf
-rw-rw-r-- 2 upalabdha upalabdha  905 Nov  8 09:45 meta.yml
-rw-rw-r-- 2 upalabdha upalabdha  673 Nov  8 09:45 params.config
-rw-rw-r-- 2 upalabdha upalabdha 8.7K Nov  8 09:45 params.json
-rw-rw-r-- 2 upalabdha upalabdha 2.6K Nov  8 09:45 test.nf
-rw-rw-r-- 2 upalabdha upalabdha  31K Nov  8 09:45 test.yml

rpetit3 commented 1 year ago

Another (trying to get an idea on how things look

ls -lh /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/./workflows/../modules/local/bactopia/assemble_genome/../../../

UpalabdhaD commented 1 year ago

Sure!!

❯ ls -lh /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/./workflows/../modules/local/bactopia/assemble_genome/../../../
total 8.0K
drwxr-xr-x  3 upalabdha upalabdha 4.0K Nov 19 19:55 local
drwxr-xr-x 57 upalabdha upalabdha 4.0K Nov 19 19:55 nf-core

rpetit3 commented 1 year ago

Did you by chance build the dev version of bactopia?

UpalabdhaD commented 1 year ago

yes robert. Initially I tried the main version, then faced issues, found one relevant solution in github and then followed this instruction.

https://github.com/bactopia/bactopia/issues/365

rpetit3 commented 1 year ago

Cool, I just pushed a fix to the dev branch: https://github.com/bactopia/bactopia/commit/4e50be9c54d200655662c3fee6e24fb59c297bf1

I'm re-building now, and it should hopefully be done in ~10 minutes

UpalabdhaD commented 1 year ago

Many thanks! Please guide me through it.

rpetit3 commented 1 year ago

OK, you might be able to just update.

conda activate bactopia
conda update -c rpetit3 -c conda-forge -c bioconda bactopia

This should hopefully recognize the updated package

UpalabdhaD commented 1 year ago

Hi @rpetit3

Is it you are talking about ?

UpalabdhaD commented 1 year ago

Hi @rpetit3

Did:

conda activate bactopia conda update -c rpetit3 -c conda-forge -c bioconda bactopia

Now:

` ❯ conda update -c rpetit3 -c conda-forge -c bioconda bactopia Collecting package metadata (current_repodata.json): done Solving environment: done

All requested packages already installed.

Retrieving notices: ...working... done `

after that:

time bactopia \ --accessions $Ralstonia_seq/Ralstonia_ENA-accessions.txt \ --use_ena \ --datasets $BaDs/ \ --species "Ralstonia solanacearum" \ --genome_size 5500000 \ --coverage 50 \ --cleanup_workdir \ --outdir $Bactopia_top/trial_11

Got the same error:

❯ bash 03_script/bactopia_rso.sh 2022-11-22 13:43:52:root:INFO - Checking if environment pre-builds are needed, use --verbose to see full details. 2022-11-22 13:43:52:root:INFO - Found Conda environments in /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/conda/envs, if a complete rebuild is needed please use --force_rebuild N E X T F L O W ~ version 22.10.1 Launching/home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/main.nf` [furious_jones] DSL2 - revision: 145bb11899

| | _ | | __ (_)
| ' \ / ` |/ | / | ' | |/ ` |
| |) | (| | (| || () | |) | | (| |
|./ _,|_|__/| ./||_,| |_|
bactopia v2.1.1 Bactopia is a flexible pipeline for complete analysis of bacterial genomes.

Core Nextflow options runName : furious_jones launchDir : /home/upalabdha/Documents/01_Work_nucleix/02_Prj_Rso_WGS/Bactopia_Rso workDir : /home/upalabdha/Documents/01_Work_nucleix/02_Prj_Rso_WGS/Bactopia_Rso/work projectDir : /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x userName : upalabdha profile : standard configFiles : /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/nextflow.config

Required Parameters accessions : /home/upalabdha/Documents/01_Work_nucleix/02_Prj_Rso_WGS/Bactopia_Rso/05_Ralstonia_sequences/Ralstonia_ENA-accessions.txt

Dataset Parameters datasets : /home/upalabdha/Documents/01_Work_nucleix/02_Prj_Rso_WGS/Bactopia_Rso/02_Ralstonia_dataset/ species : Ralstonia solanacearum coverage : 50 genome_size : 5500000

Gather Samples Parameters use_ena : true

Optional Parameters outdir : /home/upalabdha/Documents/01_Work_nucleix/02_Prj_Rso_WGS/Bactopia_Rso/trial_11

Nextflow Configuration Parameters cleanup_workdir : true

Nextflow Profile Parameters condadir : /home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/conda/envs registry : quay singularity_cache: /home/upalabdha/.bactopia/singularity

!! Only displaying parameters that differ from the pipeline defaults !!

If you use bactopia for your analysis please cite:

Bactopia https://doi.org/10.1128/mSystems.00190-20
The nf-core framework https://doi.org/10.1038/s41587-020-0439-x
Software dependencies https://bactopia.github.io/acknowledgements/

WARN: WARN: Conda Disclaimer WARN: WARN: If you have access to Docker or Singularity, please consider WARN: running Bactopia using containers. The containers are less WARN: susceptible to Conda environment related issues (e.g. version WARN: conflicts) and errors caused by creation of conda environments WARN: in parallel (use '--max_cpus 1' to over come this error). WARN: WARN: To use containers, you can use the profile parameter WARN: Docker: -profile docker WARN: Singularity: -profile singularity WARN:

Unable to read script: '/home/upalabdha/anaconda3/envs/bactopia/share/bactopia-2.1.x/./workflows/../modules/local/bactopia/assemble_genome/main.nf' -- cause: Can't find a matching module file for include: ../../../lib/nf/functions

real 0m6.620s user 0m38.313s sys 0m1.565s `

rpetit3 commented 1 year ago

Hi @UpalabdhaD

I've released v2.2.0, I'd recommend giving it a try.

Cheers, Robert

rpetit3 commented 5 months ago

Hi @UpalabdhaD

I'm cleaning up old issues and since this is related to v2, I'm going to go ahead and close this with the recommendation to give v3 a try.

Please reach out if you have any questions or issues!

Cheers, Robert

bactopia / bactopia

Unable to run Bactopia 2.1.x: downloaded and set up through conda [question] #371

1. my shell script

Source conda shell

include proxy for downloading data

Directory paths

activate conda enviornment

Build Datasets

Query ENA for all Ralstonia Sequence projects

taxonomy id for R.solanacerum is 305

Run bactopia command

Bash Output:

| | _ | | __ (_)
| ' \ / ` |/ | / | ' | |/ ` |
| |) | (| | (| || () | |) | | (| |
|./ _,|_|__/| ./||_,| |_|
bactopia v2.1.1 Bactopia is a flexible pipeline for complete analysis of bacterial genomes.

!! Only displaying parameters that differ from the pipeline defaults !!

Software dependencies https://bactopia.github.io/acknowledgements/

Did:

Now:

All requested packages already installed.

after that:

Got the same error:

| | _ | | __ (_)
| ' \ / ` |/ | / | ' | |/ ` |
| |) | (| | (| || () | |) | | (| |
|./ _,|_|__/| ./||_,| |_|
bactopia v2.1.1 Bactopia is a flexible pipeline for complete analysis of bacterial genomes.

!! Only displaying parameters that differ from the pipeline defaults !!

Software dependencies https://bactopia.github.io/acknowledgements/

bactopia / bactopia

Unable to run Bactopia 2.1.x: downloaded and set up through conda [question] #371

1. my shell script

Source conda shell

include proxy for downloading data

Directory paths

activate conda enviornment

Build Datasets

Query ENA for all Ralstonia Sequence projects

taxonomy id for R.solanacerum is 305

Run bactopia command

Bash Output:

| | _ | | __ (_) | ' \ / ` |/ | / | ' | |/ ` | | |) | (| | (| || () | |) | | (| | |./ _,|_|__/| ./||_,| |_| bactopia v2.1.1 Bactopia is a flexible pipeline for complete analysis of bacterial genomes.

!! Only displaying parameters that differ from the pipeline defaults !!

Software dependencies https://bactopia.github.io/acknowledgements/

Did:

Now:

All requested packages already installed.

after that:

Got the same error:

| | _ | | __ (_) | ' \ / ` |/ | / | ' | |/ ` | | |) | (| | (| || () | |) | | (| | |./ _,|_|__/| ./||_,| |_| bactopia v2.1.1 Bactopia is a flexible pipeline for complete analysis of bacterial genomes.

!! Only displaying parameters that differ from the pipeline defaults !!

Software dependencies https://bactopia.github.io/acknowledgements/

| | _ | | __ (_)
| ' \ / ` |/ | / | ' | |/ ` |
| |) | (| | (| || () | |) | | (| |
|./ _,|_|__/| ./||_,| |_|
bactopia v2.1.1 Bactopia is a flexible pipeline for complete analysis of bacterial genomes.

| | _ | | __ (_)
| ' \ / ` |/ | / | ' | |/ ` |
| |) | (| | (| || () | |) | | (| |
|./ _,|_|__/| ./||_,| |_|
bactopia v2.1.1 Bactopia is a flexible pipeline for complete analysis of bacterial genomes.