conda install error

[rob123king]

I have the below error when run the test command in conda for first time. I try installing SortMeRNA to my conda environment thinking it would install this too and bypass problem but I still can't find the script, any ideas where I can find it to update my conda envrionment with it, or should it just install itself during test?

command not found: indexdb_rna

Full error: Workflow execution completed unsuccessfully! The exit status of the task that caused the workflow execution to fail was: 127.

The full error message was:

Error executing process > 'download_sortmerna:sortmernaGet'

Caused by: Process download_sortmerna:sortmernaGet terminated with an error exit status (127)

Command executed:

git clone https://github.com/biocore/sortmerna.git indexdb_rna --ref ./sortmerna/data/rRNA_databases/silva-bac-16s-id90.fasta,./sortmerna/data/rRNA_databases/silva-bac-16s-id90:./sortmerna/data/rRNA_databases/silva-bac-23s-id98.fasta,./sortmerna/data/rRNA_databases/silva-bac-23s-id98:./sortmerna/data/rRNA_databases/silva-arc-16s-id95.fasta,./sortmerna/data/rRNA_databases/silva-arc-16s-id95:./sortmerna/data/rRNA_databases/silva-arc-23s-id98.fasta,./sortmerna/data/rRNA_databases/silva-arc-23s-id98:./sortmerna/data/rRNA_databases/silva-euk-18s-id95.fasta,./sortmerna/data/rRNA_databases/silva-euk-18s-id95:./sortmerna/data/rRNA_databases/silva-euk-28s-id98.fasta,./sortmerna/data/rRNA_databases/silva-euk-28s-id98:./sortmerna/data/rRNA_databases/rfam-5s-database-id98.fasta,./sortmerna/data/rRNA_databases/rfam-5s-database-id98:./sortmerna/data/rRNA_databases/rfam-5.8s-database-id98.fasta,./sortmerna/data/rRNA_databases/rfam-5.8s-database-id98 -v mv sortmerna/data/rRNA_databases . tar zcvf rRNA_databases.tar.gz rRNA_databases rm -r rRNA_databases rm -r sortmerna

Command exit status: 127

Command output: (empty)

Command error: .command.sh: line 2: git: command not found

[rob123king]

tried to get round it by using my local sortMeRNA installation that has it and see if that works

[rob123king]

still fails, but just run these commands locally so hoping it will just detect and skip this step. module load SortMeRNA/2.1-foss-2018b indexdb_rna --ref ./sortmerna/data/rRNA_databases/silva-bac-16s-id90.fasta,./sortmerna/data/rRNA_databases/silva-bac-16s-id90:./sortmerna/data/rRNA_databases/silva-bac-23s-id98.fasta,./sortmerna/data/rRNA_databases/silva-bac-23s-id98:./sortmerna/data/rRNA_databases/silva-arc-16s-id95.fasta,./sortmerna/data/rRNA_databases/silva-arc-16s-id95:./sortmerna/data/rRNA_databases/silva-arc-23s-id98.fasta,./sortmerna/data/rRNA_databases/silva-arc-23s-id98:./sortmerna/data/rRNA_databases/silva-euk-18s-id95.fasta,./sortmerna/data/rRNA_databases/silva-euk-18s-id95:./sortmerna/data/rRNA_databases/silva-euk-28s-id98.fasta,./sortmerna/data/rRNA_databases/silva-euk-28s-id98:./sortmerna/data/rRNA_databases/rfam-5s-database-id98.fasta,./sortmerna/data/rRNA_databases/rfam-5s-database-id98:./sortmerna/data/rRNA_databases/rfam-5.8s-database-id98.fasta,./sortmerna/data/rRNA_databases/rfam-5.8s-database-id98 -v mv sortmerna/data/rRNA_databases . tar zcvf rRNA_databases.tar.gz rRNA_databases rm -r rRNA_databases rm -r sortmerna srun nextflow run hoelzer-lab/rnaflow -profile test,conda,local

[rob123king]

I did the process manually out of nextflow but still tries to run it and fails.

[hoelzer]

Hi @rob123king ! Thanks for your interest in the pipeline!

So your first error seems related to

.command.sh: line 2: git: command not found

We actually don't install git in the necessary conda environment because normally this is just installed on Linux systems.

Hm actually @fischer-hub we could add this to the conda envs where we use git in the corresponding process: https://anaconda.org/anaconda/git

Nevertheless, to check this right now you @rob123king could try to install git on your system, which is anyway handy to clone other tools and code. Once you have this, please try to run the text profile again

[fischer-hub]

@rob123king It also seems like sortmerna is not installed correctly in the conda environment.

command not found: indexdb_rna

You can try to delete the environment that was created for sortmerna while running the pipeline. Then just run it again so nextflow will recreate the environment, sometimes environments get built incorrectly and you have to manually delete them.

[rob123king]

git in on the system so weird that's coming as an error and when I load the sortmerna module on our system to bypass then it picks up the command but when I run the nextflow it doesn't work. I'll try a fresh install of the conda environment and see if just starting again it all works fine. almost seems like the conda tools are not being found. Maybe as I am loading conda via our easybuild "module load miniconda" something going wrong using this route rather than local installation.

[rob123king]

Having a right drama trying to get this working via conda so just going to install myself via conda and set it to assume everything is in path and should be all fine. I've tried it on AWS batch and tower and worked really well. I would like the additional RNA-seq diff expression module at the end like UCL have and previous discussions but guess I'll hack my own version of UCL and get that working if I can.

[hoelzer]

Hi @rob123king , alright, thanks for the feedback and srry that it will just not work with conda out of the box. But nice AWS and nf-tower run. Cheers