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roland-rad-lab / MoCaSeq

Analysis pipelines for cancer genome sequencing in mice.
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Unable to create bam files #1

Closed nilesh-iiita closed 4 years ago

nilesh-iiita commented 4 years ago

No matter what dataset I try I am getting the same error and even with the test dataset.

The command I used is: sudo docker run -v ${working_directory}:/var/pipeline/ rolandradlab/mocaseq --test yes @sebastianlange

+------------+ | FILE ERROR | +------------+ Cannot access BAM file (/var/pipeline/MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam). It either does not exist or is not readable.

Please find the log file in the attachment. MoCaSeq_Test.report.txt

sebastianlange commented 4 years ago

Hi Nilesh,

Could you please provide the reference creation log:

ref/GRCm38.p6/GetReferenceData.txt

Best Sebastian

On 19. Aug 2020, at 00:20, Nilesh Kumar notifications@github.com wrote:

 No matter what dataset I try I am getting the same error and even with the test dataset.

The command I used is: sudo docker run -v ${working_directory}:/var/pipeline/ rolandradlab/mocaseq --test yes @sebastianlange

+------------+ | FILE ERROR | +------------+ Cannot access BAM file (/var/pipeline/MoCaSeq_Test/results/bam/MoCaSeq_Test.Tumor.bam). It either does not exist or is not readable.

Please find the log file in the attachment. MoCaSeq_Test.report.txt

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nilesh-iiita commented 4 years ago

Hi @sebastianlange Please find the attached GetReferenceData.txt file. GetReferenceData.txt

Thanks

sebastianlange commented 4 years ago

OK, I know what the problem is, however I currently don’t have access to my workstation. Will update with a solution in 48h.

Best Sebastian

On 19. Aug 2020, at 15:32, Nilesh Kumar notifications@github.com wrote:

 Hi @sebastianlange Please find the attached GetReferenceData.txt file. GetReferenceData.txt

Thanks

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nilesh-iiita commented 4 years ago

Hi @sebastianlange, Just checking, is docker updated?

Thanks

sebastianlange commented 4 years ago

I have just committed a bugfix (https://github.com/roland-rad-lab/MoCaSeq/releases/tag/v0.4.53). The corresponding docker container has been successfully generated (0.4.53: https://hub.docker.com/repository/docker/rolandradlab/mocaseq/builds).

1) Please remove the "ref" folder which was generated using an earlier iteration of the pipeline. 2) Pull the newest version: sudo docker pull rolandradlab/mocaseq:0.4.53 or :latest 3) Run the "test" sample again

Sorry for the inconvenience.