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Hi,
I am trying to run your ATAC-seq pipeline and always crush with the same error. (Fatal error: atac.bds, line 1216, pos 2. Cannot allocate memory.)
I have followed the instruction that are in the…
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OS or Platform: CentOS Linux release 7.4.1708
Cromwell/dxWDL version: cromwell-34.jar
Conda version: conda 4.3.30
I am trying to run the chip-seq pipeline on the test data (ENCSR936XTK) as per th…
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Hi,
first and foremost, thank you so much for this pipeline. Standardization is much needed in the ATAC-seq world. I am however encountering an issue in the qc-step that I am too much a beginner for …
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Thanks for developing this great pipeline! I noticed something with my data
I sequenced my samples twice, once with 100PE and once with 75PE. I did the atac-seq analysis in two different ways:
(1)…
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Hi,
I'm trying to run the ATAC-Seq pipeline on SCG, and am hitting an error at the adapter trimming step: 'sbatch: error: Unable to open file smontgom ' (smontgom is my PI/account name). My comman…
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Hi, I am trying to run chipseq_pipeline using more than 2 replicates using the command as below. But it seems that the program can not take more than 2 replicates. I also attached part of the log fi…
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Hi, Jin,
thanks a lot for your previous help with the "six" package, that resolved the ATAQC errors.
another question (hopefully the last) i want to ask is, how to specify an input sample as con…
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The pipeline seems to be working fine generally, but I can't get any broadpeaks or gapped peaks after finishing the whole pipeline.
--------------------Stderr--------------------
INFO @ Wed, 09 M…
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For the first public release of our pipeline, we should make it independent using docker and conda.. Then we can also see whether we can add some some travis tests (issue #34) .
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Here is my pipeline's workflow option for cromwell. Cromwell automatically ignores runtime attributes that are not supported by a specific backend. So I can use one file for multiple backends (google …