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Teichlab / bracer

BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data
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Docker image Trinity "No recombinats found" #45

Closed SabrinaITNL closed 4 years ago

SabrinaITNL commented 4 years ago

Hi, I am running Bracer on the docker image. I already tried two files and they both stop at the Trinity step with the following comment: Trinity run failed. Must investigate error above. Trinity failed for locus No successful Trinity assemblies

No recombinants found

Any idea on how can I solve this? Thanks! :) Sabrina

mstubb commented 4 years ago

Does bracer test work on your docker image now?

If so, can you run on all your cells? It may be that the two you've tried just don't contain sequences that can be assembled.

M

On 29 Jan 2020, at 11:19, SabrinaITNL notifications@github.com wrote:

Hi, I am running Bracer on the docker image. I already tried two files and they both stop at the Trinity step with the following comment: Trinity run failed. Must investigate error above. Trinity failed for locus No successful Trinity assemblies

No recombinants found

Any idea on how can I solve this? Thanks! :) Sabrina

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SabrinaITNL commented 4 years ago

Hi Mike, nope, also the test fails. Might it be because the memory allocated to the VM is too little? Which is the minimum amount required? Cheers Sabrina

mstubb commented 4 years ago

Ah, yes. That could well be why. Can you try 6 or 8GB?

Mike

On 29 Jan 2020, at 12:22, SabrinaITNL notifications@github.com wrote:

Hi Mike, nope, also the test fails. Might it be because the memory allocated to the VM is too little? Which is the minimum amount required? Cheers Sabrina

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