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o-william-white / skim2mito

A snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes from genome skims
MIT License
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Stuck on downloading the vole data #4

Closed rvosa closed 1 year ago

rvosa commented 1 year ago

Hi,

when I try to run the code block about downloading example data my miniconda doesn't like the arguments. What do you think might be going on?

$ conda env create -n sra-tools -c bioconda                                                                                    
usage: conda-env [-h] {create,export,list,remove,update,config} ...                                                                                                                   
conda-env: error: unrecognized arguments: -c
o-william-white commented 1 year ago

I think this should be as follows: ''' conda create -n sra-tools -c bioconda sra-tools ''' Away from my laptop but will confirm tomorrow.

o-william-white commented 1 year ago

Updated the README, thanks for highlighting this.

rvosa commented 1 year ago

OK cool, that makes sense. With that sorted, I am now stuck on the actual downloading. Here's what I'm getting:

fetching reads for SRR5201684
2023-04-19T09:50:46 fastq-dump.2.8.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed )
2023-04-19T09:50:46 fastq-dump.2.8.0 sys: mbedtls_ssl_get_verify_result returned 0x8 (  !! The certificate is not correctly signed by the trusted CA  )
2023-04-19T09:50:46 fastq-dump.2.8.0 err: item not found while constructing within virtual database module - the path 'SRR5201684' cannot be opened as database or table

So there's something wrong with validating the SSL certificates. This is on a virgin-ish Ubuntu 22.04LTS. I tried to update the certificates:

sudo apt-get update
sudo apt-get install --reinstall ca-certificates
sudo update-ca-certificates

And restarted the server, to no avail. Any idea how to fix that?

o-william-white commented 1 year ago

Not an error I have found before. Is it simply a network connection issue? I found this issue which seemed related https://github.com/ncbi/sra-tools/issues/139

Also, it looks like conda has installed a sligtly older version or sra-tools. I wonder if using the most recent version might help? 

 conda create -n sra-tools -c bioconda sra-tools=3.0.3
rvosa commented 1 year ago

It is indeed a version issue: I Frankensteined fastq-dump onto the server using NCBI's binaries and then the download proceeds. When we try to do it the correct way via conda we seem to enter into dependency hell: it wants to update libgcc-ng and that seems like a scary thing to do.