Closed pavlo888 closed 7 months ago
Hi @pavlo888
Can you verify the version number?
Thanks!
Using the latest version (v2.0.1) of fastq-dl I can't reproduce this error
fastq-dl -a SRR12333278 --provider sra
Downloads the fastqs no problem.
Given your command line usage, I suspect you're using an old version @pavlo888?
Hi @rpetit3,
I have checked my current fast-dl version and it is 1.1.1. I have installed this version following the conda recipe as suggested in the GitHub.
(fastq-dl) pavlo@Pablos-MacBook-Air sra-reads-amf-lsu % fastq-dl --version fastq-dl 1.1.1
How could I update the current version?
What happens when you run conda install fastq-dl=2.0
?
When I do the command
conda install fastq-dl=2.0
I get
`Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: `
Mind you I already added the channels bioconda and conda-forge
Hmm weird. Is this an environment with other packages in it or a new one just for fastq-dl? What is the python version in the environment?
Agree with @mbhall88
At this point it might be easier to create a new environment:
# If ok overwriting existing
mamba create -n fastq-dl 'fastq-dl=2.0.1'
# else
mamba create -n fastq-dl-v2 'fastq-dl=2.0.1'
@mbhall88
I tried to create a new environment for the new fastq-dl version. The python version is 3.9.6
@rpetit3 I have tried creating a new environment with mamba and I got the following error `Could not solve for environment specs Encountered problems while solving:
The environment can't be solved, aborting the operation`
Perhaps I should also mention that I am on a Mac environment.
There's our issue. Looks like sra-tools is not built for OSX
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/sra-tools/meta.yaml#L14-L16
Might have to go the docker route for the time being. I'll see if there are any folks on the SRA/NCBI side interested in fixing the build for OSX.
The newer versions of sra-tools no longer require the manual user interaction (haha had to implement a hacky solution to avoid this)
I see. Thanks for helping me out on this one.
Is there any place where I can find the documentation for using the docker image of fastq-dl? I have only found this repository https://hub.docker.com/r/biodancer/fastq-dl/tags but I am not so sure it is the right one.
I am not sure how to mount my working directory to the image and start downloading some SRA files.
No problem, you'll want the one from biocontainers, as it's based on the Bioconda build.
docker pull quay.io/biocontainers/fastq-dl:2.0.1--pyhdfd78af_0
Then something like this to download to ${PWD}
docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data quay.io/biocontainers/fastq-dl:2.0.1--pyhdfd78af_0 \
fastq-dl --accession SRR10532144 --outdir /data/SRR10532144
Hi @pavlo888,
I think this might have gotten sorted, if not, please feel free to reopen!
Cheers, Robert
Hi @rpetit3
I am very excited to use the fastq-dl tool to download some SRA data but I am having some issues.
When I run the following command:
fastq-dl SRR12333278 SRA
I get the following error:2023-05-29 00:26:51:root:ERROR - There was an issue querying ENA, exiting... 2023-05-29 00:26:51:root:ERROR - STATUS: 400 2023-05-29 00:26:51:root:ERROR - TEXT: Invalid fieldName(s) supplied: cram_index_ftp,cram_index_aspera,cram_index_galaxy
I thought I might be having some connection issues with the Aspera Connect tool (ascp). However, this tool is already in my current temporary path since after running the command "echo $PATH" I get:
/Users/pavlo/mambaforge/envs/fastq-dl/bin:/Users/pavlo/mambaforge/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/Aspera
Any idea what the problem might be?