Error STATUS 400

Question

Error STATUS 400

pavlo888 opened this issue a year ago · comments

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?

Robert A. Petit III · Answer 1 · Mon May 29 2023 12:40:25 GMT+0800 (China Standard Time)

Hi @pavlo888

Can you verify the version number?

Thanks!

Michael Hall · Answer 2 · Tue May 30 2023 07:53:16 GMT+0800 (China Standard Time)

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?

pavlo888 · Answer 3 · Tue May 30 2023 12:00:58 GMT+0800 (China Standard Time)

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?

Michael Hall · Answer 4 · Wed May 31 2023 07:03:21 GMT+0800 (China Standard Time)

What happens when you run conda install fastq-dl=2.0?

pavlo888 · Answer 5 · Wed May 31 2023 12:15:50 GMT+0800 (China Standard Time)

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

Michael Hall · Answer 6 · Wed May 31 2023 12:26:46 GMT+0800 (China Standard Time)

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?

Robert A. Petit III · Answer 7 · Wed May 31 2023 12:44:21 GMT+0800 (China Standard Time)

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'

pavlo888 · Answer 8 · Wed May 31 2023 22:36:47 GMT+0800 (China Standard Time)

@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:

nothing provides sra-tools >=3.0.1 needed by fastq-dl-2.0.1-pyhdfd78af_0

The environment can't be solved, aborting the operation`

Perhaps I should also mention that I am on a Mac environment.

Robert A. Petit III · Answer 9 · Wed May 31 2023 23:02:07 GMT+0800 (China Standard Time)

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)

pavlo888 · Answer 10 · Fri Jun 02 2023 09:08:11 GMT+0800 (China Standard Time)

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.

Robert A. Petit III · Answer 11 · Fri Jun 02 2023 11:14:37 GMT+0800 (China Standard Time)

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

Robert A. Petit III · Answer 12 · Thu Feb 29 2024 01:12:40 GMT+0800 (China Standard Time)

Hi @pavlo888,

I think this might have gotten sorted, if not, please feel free to reopen!

Cheers,
Robert