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Teichlab / bracer

BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data
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Docker image: FASTQ not found #44

Closed SabrinaITNL closed 4 years ago

SabrinaITNL commented 4 years ago

Hi, I tried to install and run Bracer but got stuck with an issue that is still unanswered (Issue#43, https://github.com/Teichlab/bracer/issues/43).

Therefore I tried to run the DOCKER image but got this error: OSError: [Errno 2] FASTQ file not found.

The command I used is: docker run -it --rm -v $PWD:/scratch -w /scratch teichlab/bracer assemble --single_end --fragment_length 75 --fragment_sd 1 A1 output SS2-18-006-A1_S1_merged_R1_001.fastq

Any idea why the FASTQ file can't be found?

Thank you for the help!

Best regards, Sabrina

mstubb commented 4 years ago

Are you running that command from within the directory that contains the file A1 output SS2-18-006-A1_S1_merged_R1_001.fastq?

If so I think the spaces in the file name are probably breaking it, try putting quotes around the file name or renaming to remove spaces.

Mike

On 22 Jan 2020, at 11:15, SabrinaITNL notifications@github.com wrote:

Hi, I tried to install and run Bracer but got stuck with an issue that is still unanswered (Issue#43, #43 https://github.com/Teichlab/bracer/issues/43).

Therefore I tried to run the DOCKER image but got this error: OSError: [Errno 2] FASTQ file not found.

The command I used is: docker run -it --rm -v $PWD:/scratch -w /scratch teichlab/bracer assemble --single_end --fragment_length 75 --fragment_sd 1 A1 output SS2-18-006-A1_S1_merged_R1_001.fastq

Any idea why the FASTQ file can't be found?

Thank you for the help!

Best regards, Sabrina

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SabrinaITNL commented 4 years ago

Hi Mike, the file name is SS2-18-006-A1_S1_merged_R1_001.fastq. A1 and output ate the of the assemble command.

And yes I am running the command from the directory that contains the fastq file. I am using the Docker toolbox on windows. The directory is a mounted directory (so added as shared folder).

I hope this is enough informatio. BW Sabrina

mstubb commented 4 years ago

Does docker run -it --rm -v $PWD:/scratch -w /scratch teichlab/bracer test -o test_data work if you run it from the directory into which you cloned BraCeR?

M

On 22 Jan 2020, at 11:21, SabrinaITNL notifications@github.com wrote:

Hi Mike, the file name is SS2-18-006-A1_S1_merged_R1_001.fastq. A1 and output ate the of the assemble command.

And yes I am running the command from the directory that contains the fastq file. I am using the Docker toolbox on windows. The directory is a mounted directory (so added as shared folder).

I hope this is enough informatio. BW Sabrina

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SabrinaITNL commented 4 years ago

I get this error: FileNotFoundError: [Errno 2] No such file or directory: '/scratch/test_data/results

mstubb commented 4 years ago

This is going to be very hard to debug remotely (I think it's possibly some combination of factors to do with where things are installed and how Docker is set up). Is there someone at your institute who can assist in person?

On 22 Jan 2020, at 11:28, SabrinaITNL notifications@github.com wrote:

I get this error: FileNotFoundError: [Errno 2] No such file or directory: '/scratch/test_data/results

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SabrinaITNL commented 4 years ago

Nope :( To me it looks like I can't link my working directory to the /scratch folder in the docker image. But I guess that's indeed more a "docker" problem rather then a"BraCer" problem.

Thank you anyway for your quick reply! I'll look further on how to make BraCer work on my data...

BW Sabrina

dcroote commented 4 years ago

@SabrinaITNL - I just tested the docker command:

docker run -it --rm -v $PWD:/scratch -w /scratch teichlab/bracer test -o test_data

and I believe the error you are seeing is because the test_data/results directory structure has to already exist on your local machine relative to where you are running the docker command. Try running mkdir -p test_data/results before running the above.